Molecules for diagnostics and therapeutics

ABSTRACT

The present invention provides purified human polynucleotides for diagnostics and therapeutics (dithp). Also encompassed are the polypeptides (DITHP) encoded by dithp. The invention also provides for the use of dithp, or complements, oligonucleotides, or fragments thereof in diagnostic assays. The invention further provides for vectors and host cells containing dithp for the expression of DITHP. The invention additionally provides for the use of isolated and purified DITHP to induce antibodies and to screen libraries of compounds and the use of anti-DITHP antibodies in diagnostic assays. Also provided are microarrays containing dithp and methods of use.

[0001] This application is a continuation-in-part of U.S. Ser. No. 09/980,285, filed Nov. 30, 2001, which is the National Stage of International Application No. PCT/US00/15404, filed May 31, 2000, and published in English as WO 00/73509 on Dec. 7, 2000, which claims the benefit under 35 U.S.C. § 119(e) of provisional applications U.S. Ser. No. 60/147,500, filed Aug. 5, 1999, U.S. Ser. No. 60/147,542, filed Aug. 5, 1999, U.S. Ser. No. 60/147,541, filed Aug. 5, 1999, U.S. Ser. No. 60/147,824, filed Aug. 5, 1999, U.S. Ser. No. 60/147,547, filed Aug. 5, 1999, U.S. Ser. No. 60/147,530, filed Aug. 5, 1999, U.S. Ser. No. 60/147,536, filed Aug. 5, 1999, U.S. Ser. No. 60/147,520, filed Aug. 5, 1999, U.S. Ser. No. 60/147,527, filed Aug. 5, 1999, U.S. Ser. No. 60/147,549, filed Aug. 5, 1999, U.S. Ser. No. 60/147,377, filed Aug. 4, 1999, U.S. Ser. No. 60/147,436, filed Aug. 4, 1999, U.S. Ser. No. 60/137,411, filed Jun. 3, 1999, U.S. Ser. No. 60/137,396, filed Jun. 3, 1999, U.S. Ser. No. 60/137,417, filed Jun. 3, 1999, U.S. Ser. No. 60/137,337, filed Jun. 3, 1999, U.S. Ser. No. 60/137,173, filed Jun. 2, 1999, U.S. Ser. No. 60/137,114, filed Jun. 2, 1999, U.S. Ser. No. 60/137,259, filed Jun. 2, 1999, U.S. Ser. No. 60/137,113, filed Jun. 2, 1999, U.S. Ser. No. 60/137,260, filed Jun. 2, 1999, U.S. Ser. No. 60/137,258, filed Jun. 2, 1999, U.S. Ser. No. 60/137,109, filed Jun. 2, 1999, and U.S. Ser. No. 60/137,161, filed Jun. 1, 1999.

TECHNICAL FIELD

[0002] The present invention relates to human molecules for diagnostics and therapeutics and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with human molecules.

BACKGROUND OF THE INVENTION

[0003] The human genome is comprised of thousands of genes, many encoding gene products that function in the maintenance and growth of the various cells and tissues in the body. Aberrant expression or mutations in these genes and their products is the cause of, or is associated with, a variety of human diseases such as cancer and other cell proliferative disorders, autoimmune/inflammatory disorders, infections, developmental disorders, endocrine disorders, metabolic disorders, neurological disorders, gastrointestinal disorders, transport disorders, and connective tissue disorders. The identification of these genes and their products is the basis of an ever-expanding effort to find markers for early detection of diseases, and targets for their prevention and treatment. Therefore, these genes and their products are useful as diagnostics and therapeutics. These genes may encode, for example, enzyme molecules, molecules associated with growth and development, biochemical pathway molecules, extracellular information transmission molecules, receptor molecules, intracellular signaling molecules, membrane transport molecules, protein modification and maintenance molecules, nucleic acid synthesis and modification molecules, adhesion molecules, antigen recognition molecules, secreted and extracellular matrix molecules, cytoskeletal molecules, ribosomal molecules, electron transfer associated molecules, transcription factor molecules, chromatin molecules, cell membrane molecules, and organelle associated molecules.

[0004] For example, cancer represents a type of cell proliferative disorder that affects nearly every tissue in the body. A wide variety of molecules, either aberrantly expressed or mutated, can be the cause of, or involved with, various cancers because tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals such as growth factors and other mitogens, and intracellular cues such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors. Aberrant expression or mutations in any of these gene products can result in cell proliferative disorders such as cancer. Oncogenes are genes generally derived from normal genes that, through abnormal expression or mutation, can effect the transformation of a normal cell to a malignant one (oncogenesis). Oncoproteins, encoded by oncogenes, can affect cell proliferation in a variety of ways and include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. In contrast, tumor-suppressor genes are involved in inhibiting cell proliferation. Mutations which cause reduced function or loss of function in tumor-suppressor genes result in aberrant cell proliferation and cancer. Although many different genes and their products have been found to be associated with cell proliferative disorders such as cancer, many more may exist that are yet to be discovered.

[0005] DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. A cytochrome p450 gene array is useful to determine whether individuals have one of a number of specific mutations that could result in increased drug metabolism, drug resistance or drug toxicity.

[0006] DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as when the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaling pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.

[0007] Enzyme Molecules

[0008] SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5 encode, for example, human enzyme molecules.

[0009] The cellular processes of biogenesis and biodegradation involve a number of key enzyme classes including oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. These enzyme classes are each comprised of numerous substrate-specific enzymes having precise and well regulated functions. These enzymes function by facilitating metabolic processes such as glycolysis, the tricarboxylic cycle, and fatty acid metabolism; synthesis or degradation of amino acids, steroids, phospholipids, alcohols, etc.; regulation of cell signalling, proliferation, inflamation, apoptosis, etc., and through catalyzing critical steps in DNA replication and repair, and the process of translation.

[0010] Oxidoreductases

[0011] Many pathways of biogenesis and biodegradation require oxidoreductase (dehydrogenase or reductase) activity, coupled to the reduction or oxidation of a donor or acceptor cofactor. Potential cofactors include cytochromes, oxygen, disulfide, iron-sulfur proteins, flavin adenine dinucleotide (FAD), and the nicotinamide adenine dinucleotides NAD and NADP (Newsholme, E. A. and A. R. Leech (1983) Biochemistry for the Medical Sciences, John Wiley and Sons, Chichester, U.K., pp. 779-793). Reductase activity catalyzes the transfer of electrons between substrate(s) and cofactor(s) with concurrent oxidation of the cofactor. The reverse dehydrogenase reaction catalyzes the reduction of a cofactor and consequent oxidation of the substrate. Oxidoreductase enzymes are a broad superfamily of proteins that catalyze numerous reactions in all cells of organisms ranging from bacteria to plants to humans. These reactions include metabolism of sugar, certain detoxification reactions in the liver, and the synthesis or degradation of fatty acids, amino acids, glucocorticoids, estrogens, androgens, and prostaglandins. Different family members are named according to the direction in which their reactions are typically catalyzed; thus they may be referred to as oxidoreductases, oxidases, reductases, or dehydrogenases. In addition, family members often have distinct cellular localizations, including the cytosol, the plasma membrane, mitochondrial inner or outer membrane, and peroxisomes.

[0012] Short-chain alcohol dehydrogenases (SCADs) are a family of dehydrogenases that only share 15% to 30% sequence identity, with similarity predominantly in the coenzyme binding domain and the substrate binding domain. In addition to the well-known role in detoxification of ethanol, SCADs are also involved in synthesis and degradation of fatty acids, steroids, and some prostaglandins, and are therefore implicated in a variety of disorders such as lipid storage disease, myopathy, SCAD deficiency, and certain genetic disorders. For example, retinol dehydrogenase is a SCAD-family member (Simon, A. et al. (1995) J. Biol. Chem. 270:1107-1112) that converts retinol to retinal, the precursor of retinoic acid. Retinoic acid, a regulator of differentiation and apoptosis, has been shown to down-regulate genes involved in cell proliferation and inflammation (Chai, X. et al. (1995) J. Biol. Chem. 270:3900-3904). In addition, retinol dehydrogenase has been linked to hereditary eye diseases such as autosomal recessive childhood-onset severe retinal dystrophy (Simon, A. et al. (1996) Genomics 36:424-430).

[0013] Propagation of nerve impulses, modulation of cell proliferation and differentiation, induction of the immune response, and tissue homeostasis involve neurotransmitter metabolism (Weiss, B. (1991) Neurotoxicology 12:379-386; Collins, S. M. et al. (1992) Ann. N.Y. Acad. Sci. 664:415-424; Brown, J. K. and H. Imam (1991) J. Inherit. Metab. Dis. 14:436-458). Many pathways of neurotransmitter metabolism require oxidoreductase activity, coupled to reduction or oxidation of a cofactor, such as NAD⁺/NADH (Newsholme, E. A. and A. R. Leech (1983) Biochemistry for the Medical Sciences, John Wiley and Sons, Chichester, U.K. pp. 779-793). Degradation of catecholamines (epinephrine or norepinephrine) requires alcohol dehydrogenase (in the brain) or aldehyde dehydrogenase (in peripheral tissue). NAD+-dependent aldehyde dehydrogenase oxidizes 5-hydroxyindole-3-acetate (the product of 5-hydroxytryptamine (serotonin) metabolism) in the brain, blood platelets, liver and pulmonary endothelium (Newsholme, supra, p. 786). Other neurotransmitter degradation pathways that utilize NAD⁺/NADH-dependent oxidoreductase activity include those of L-DOPA (precursor of dopamine, a neuronal excitatory compound), glycine (an inhibitory neurotransmitter in the brain and spinal cord), histamine (liberated from mast cells during the inflammatory response), and taurine (an inhibitory neurotransmitter of the brain stem, spinal cord and retina) (Newsholme, supra, pp. 790, 792). Epigenetic or genetic defects in neurotransmitter metabolic pathways can result in a spectrum of disease states in different tissues including Parkinson disease and inherited myoclonus (McCance, K. L. and S. E. Huether (1994) Pathophysiology, Mosby-Year Book, Inc., St. Louis Mo., pp. 402-404; Gundlach, A. L. (1990) FASEB J. 4:2761-2766).

[0014] Tetrahydrofolate is a derivatized glutamate molecule that acts as a carrier, providing activated one-carbon units to a wide variety of biosynthetic reactions, including synthesis of purines, pyrimidines, and the amino acid methionine. Tetrahydrofolate is generated by the activity of a holoenzyme complex called tetrahydrofolate synthase, which includes three enzyme activities: tetrahydrofolate dehydrogenase, tetrahydrofolate cyclohydrolase, and tetrahydrofolate synthetase. Thus, tetrahydrofolate dehydrogenase plays an important role in generating building blocks for nucleic and amino acids, crucial to proliferating cells.

[0015] 3-Hydroxyacyl-CoA dehydrogenase (3HACD) is involved in fatty acid metabolism. It catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA, with concomitant oxidation of NAD to NADH, in the mitochondria and peroxisomes of eukaryotic cells. In peroxisomes, 3HACD and enoyl-CoA hydratase form an enzyme complex called bifunctional enzyme, defects in which are associated with peroxisomal bifunctional enzyme deficiency. This interruption in fatty acid metabolism produces accumulation of very-long chain fatty acids, disrupting development of the brain, bone, and adrenal glands. Infants born with this deficiency typically die within 6 months (Watkins, P. et al. (1989) J. Clin. Invest. 83:771-777; Online Mendelian Inheritance in Man (OMIM), #261515). The neurodegeneration that is characteristic of Alzheimer's disease involves development of extracellular plaques in certain brain regions. A major protein component of these plaques is the peptide amyloid-β(Aβ), which is one of several cleavage products of amyloid precursor protein (APP). 3HACD has been shown to bind the Aβ peptide, and is overexpressed in neurons affected in Alzheimer's disease. In addition, an antibody against 3HACD can block the toxic effects of Aβ in a cell culture model of Alzheimer's disease (Yan, S. et al. (1997) Nature 389:689-695; OMIM, #602057).

[0016] Steroids, such as estrogen, testosterone, corticosterone, and others, are generated from a common precursor, cholesterol, and are interconverted into one another. A wide variety of enzymes act upon cholesterol, including a number of dehydrogenases. Steroid dehydrogenases, such as the hydroxysteroid dehydrogenases, are involved in hypertension, fertility, and cancer (Duax, W. L. and D. Ghosh (1997) Steroids 62:95-100). One such dehydrogenase is 3-oxo-5-α-steroid dehydrogenase (OASD), a microsomal membrane protein highly expressed in prostate and other androgen-responsive tissues. OASD catalyzes the conversion of testosterone into dihydrotestosterone, which is the most potent androgen. Dihydrotestosterone is essential for the formation of the male phenotype during embryogenesis, as well as for proper androgen-mediated growth of tissues such as the prostate and male genitalia. A defect in OASD that prevents the conversion of testosterone into dihydrotestosterone leads to a rare form of male pseudohermaphroditis, characterized by defective formation of the external genitalia (Andersson, S. et al. (1991) Nature 354:159-161; Labrie, F. et al. (1992) Endocrinology 131:1571-1573; OMIM #264600). Thus, OASD plays a central role in sexual differentiation and androgen physiology.

[0017] 17β-hydroxysteroid dehydrogenase (17βHSD6) plays an important role in the regulation of the male reproductive hormone, dihydrotestosterone (DHTT). 17βHSD6 acts to reduce levels of DHTT by oxidizing a precursor of DHTT, 3α-diol, to androsterone which is readily glucuronidated and removed from tissues. 17βHSD6 is active with both androgen and estrogen substrates when expressed in embryonic kidney 293 cells. At least five other isozymes of 17βHSD have been identified that catalyze oxidation and/or reduction reactions in various tissues with preferences for different steroid substrates (Biswas, M. G. and D. W. Russell (1997) J. Biol. Chem. 272:15959-15966). For example, 17βHSD1 preferentially reduces estradiol and is abundant in the ovary and placenta. 17βHSD2 catalyzes oxidation of androgens and is present in the endometrium and placenta. 17βHSD3 is exclusively a reductive enzyme in the testis (Geissler, W. M. et al. (1994) Nat. Genet. 7:34-39). An excess of androgens such as DHTT can contribute to certain disease states such as benign prostatic hyperplasia and prostate cancer.

[0018] Oxidoreductases are components of the fatty acid metabolism pathways in mitochondria and peroxisomes. The main beta-oxidation pathway degrades both saturated and unsaturated fatty acids, while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids. The auxiliary beta-oxidation enzyme 2,4-dienoyl-CoA reductase catalyzes the removal of even-numbered double bonds from unsaturated fatty acids prior to their entry into the main beta-oxidation pathway. The enzyme may also remove odd-numbered double bonds from unsaturated fatty acids (Koivuranta, K. T. et al. (1994) Biochem. J. 304:787-792; Smeland, T. E. et al. (1992) Proc. Natl. Acad. Sci. USA 89:6673-6677). 2,4-dienoyl-CoA reductase is located in both mitochondria and peroxisomes. Inherited deficiencies in mitochondrial and peroxisomal beta-oxidation enzymes are associated with severe diseases, some of which manifest themselves soon after birth and lead to death within a few years. Defects in beta-oxidation are associated with Reye's syndrome, Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum's disease, acyl-CoA oxidase deficiency, and bifunctional protein deficiency (Suzuki, Y. et al. (1994) Am. J. Hum. Genet. 54:36-43; Hoefler, supra; Cotran, R. S. et al. (1994) Robbins Pathologic Basis of Disease, W. B. Saunders Co., Philadelphia Pa., p.866). Peroxisomal beta-oxidation is impaired in cancerous tissue. Although neoplastic human breast epithelial cells have the same number of peroxisomes as do normal cells, fatty acyl-CoA oxidase activity is lower than in control tissue (el Bouhtoury, F. et al. (1992) J. Pathol. 166:27-35). Human colon carcinomas have fewer peroxisomes than normal colon tissue and have lower fatty-acyl-CoA oxidase and bifunctional enzyme (including enoyl-CoA hydratase) activities than normal tissue (Cable, S. et al. (1992) Virchows Arch. B Cell Pathol. Incl. Mol. Pathol. 62:221-226). Another important oxidoreductase is isocitrate dehydrogenase, which catalyzes the conversion of isocitrate to a-ketoglutarate, a substrate of the citric acid cycle. Isocitrate dehydrogenase can be either NAD or NADP dependent, and is found in the cytosol, mitochondria, and peroxisomes. Activity of isocitrate dehydrogenase is regulated developmentally, and by hormones, neurotransmitters, and growth factors.

[0019] Hydroxypyruvate reductase (HPR), a peroxisomal 2-hydroxyacid dehydrogenase in the glycolate pathway, catalyzes the conversion of hydroxypyruvate to glycerate with the oxidation of both NADH and NADPH. The reverse dehydrogenase reaction reduces NAD⁺ and NADP⁺. HPR recycles nucleotides and bases back into pathways leading to the synthesis of ATP and GTP. ATP and GTP are used to produce DNA and RNA and to control various aspects of signal transduction and energy metabolism. Inhibitors of purine nucleotide biosynthesis have long been employed as antiproliferative agents to treat cancer and viral diseases. HPR also regulates biochemical synthesis of serine and cellular serine levels available for protein synthesis.

[0020] The mitochondrial electron transport (or respiratory) chain is a series of oxidoreductase-type enzyme complexes in the mitochondrial membrane that is responsible for the transport of electrons from NADH through a series of redox centers within these complexes to oxygen, and the coupling of this oxidation to the synthesis of ATP (oxidative phosphorylation). ATP then provides the primary source of energy for driving a cell's many energy-requiring reactions. The key complexes in the respiratory chain are NADH:ubiquinone oxidoreductase (complex I), succinate:ubiquinone oxidoreductase (complex II), cytochrome c₁-b oxidoreductase (complex III), cytochrome c oxidase (complex IV), and ATP synthase (complex V) (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York N.Y., pp. 677-678). All of these complexes are located on the inner matrix side of the mitochondrial membrane except complex II, which is on the cytosolic side.

[0021] Complex II transports electrons generated in the citric acid cycle to the respiratory chain. The electrons generated by oxidation of succinate to fumarate in the citric acid cycle are transferred through electron carriers in complex II to membrane bound ubiquinone (Q). Transcriptional regulation of these nuclear-encoded genes appears to be the predominant means for controlling the biogenesis of respiratory enzymes. Defects and altered expression of enzymes in the respiratory chain are associated with a variety of disease conditions.

[0022] Other dehydrogenase activities using NAD as a cofactor are also important in mitochondrial function. 3-hydroxyisobutyrate dehydrogenase (3HBD), important in valine catabolism, catalyzes the NAD-dependent oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde within mitochondria. Elevated levels of 3-hydroxyisobutyrate have been reported in a number of disease states, including ketoacidosis, methylmalonic acidemia, and other disorders associated with deficiencies in methylmalonate semialdehyde dehydrogenase (Rougraff, P. M. et al. (1989) J. Biol. Chem. 264:5899-5903).

[0023] Another mitochondrial dehydrogenase important in amino acid metabolism is the enzyme isovaleryl-CoA-dehydrogenase (IVD). IVD is involved in leucine metabolism and catalyzes the oxidation of isovaleryl-CoA to 3-methylcrotonyl-CoA. Human IVD is a tetrameric flavoprotein that is encoded in the nucleus and synthesized in the cytosol as a 45 kDa precursor with a mitochondrial import signal sequence. A genetic deficiency, caused by a mutation in the gene encoding IVD, results in the condition known as isovaleric acidemia. This mutation results in inefficient mitochondrial import and processing of the IVD precursor (Vockley, J. et al. (1992) J. Biol. Chem. 267:2494-2501).

[0024] Transferases

[0025] Transferases are enzymes that catalyze the transfer of molecular groups. The reaction may involve an oxidation, reduction, or cleavage of covalent bonds, and is often specific to a substrate or to particular sites on a type of substrate. Transferases participate in reactions essential to such functions as synthesis and degradation of cell components, regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Transferases are involved in key steps in disease processes involving these functions. Transferases are frequently classified according to the type of group transferred. For example, methyl transferases transfer one-carbon methyl groups, amino transferases transfer nitrogenous amino groups, and similarly denominated enzymes transfer aldehyde or ketone, acyl, glycosyl, alkyl or aryl, isoprenyl, saccharyl, phosphorous-containing, sulfur-containing, or selenium-containing groups, as well as small enzymatic groups such as Coenzyme A.

[0026] Acyl transferases include peroxisomal carnitine octanoyl transferase, which is involved in the fatty acid beta-oxidation pathway, and mitochondrial carnitine palmitoyl transferases, involved in fatty acid metabolism and transport. Choline O-acetyl transferase catalyzes the biosynthesis of the neurotransmitter acetylcholine.

[0027] Amino transferases play key roles in protein synthesis and degradation, and they contribute to other processes as well. For example, the amino transferase 5-aminolevulinic acid synthase catalyzes the addition of succinyl-CoA to glycine, the first step in heme biosynthesis. Other amino transferases participate in pathways important for neurological function and metabolism. For example, glutamine-phenylpyruvate amino transferase, also known as glutamine transaminase K (GTK), catalyzes several reactions with a pyridoxal phosphate cofactor. GTK catalyzes the reversible conversion of L-glutamine and phenylpyruvate to 2-oxoglutaramate and L-phenylalanine. Other amino acid substrates for GTK include L-methionine, L-histidine, and L-tyrosine. GTK also catalyzes the conversion of kynurenine to kynurenic acid, a tryptophan metabolite that is an antagonist of the N-methyl-D-aspartate (NMDA) receptor in the brain and may exert a neuromodulatory function. Alteration of the kynurenine metabolic pathway may be associated with several neurological disorders. GTK also plays a role in the metabolism of halogenated xenobiotics conjugated to glutathione, leading to nephrotoxicity in rats and neurotoxicity in humans. GTK is expressed in kidney, liver, and brain. Both human and rat GTKs contain a putative pyridoxal phosphate binding site (ExPASy ENZYME: EC 2.6.1.64; Perry, S. J. et al. (1993) Mol. Pharmacol. 43:660-665; Perry, S. et al. (1995) FEBS Lett. 360:277-280; and Alberati-Giani, D. et al. (1995) J. Neurochem. 64:1448-1455). A second amino transferase associated with this pathway is kynurenine/α-aminoadipate amino transferase (AadAT). AadAT catalyzes the reversible conversion of a-aminoadipate and α-ketoglutarate to α-ketoadipate and L-glutamate during lysine metabolism. AadAT also catalyzes the transamination of kynurenine to kynurenic acid. A cytosolic AadAT is expressed in rat kidney, liver, and brain (Nakatani, Y. et al. (1970) Biochim. Biophys. Acta 198:219-228; Buchli, R. et al. (1995) J. Biol. Chem. 270:29330-29335).

[0028] Glycosyl transferases include the mammalian UDP-glucouronosyl transferases, a family of membrane-bound microsomal enzymes catalyzing the transfer of glucouronic acid to lipophilic substrates in reactions that play important roles in detoxification and excretion of drugs, carcinogens, and other foreign substances. Another mammalian glycosyl transferase, mammalian UDP-galactose-ceramide galactosyl transferase, catalyzes the transfer of galactose to ceramide in the synthesis of galactocerebrosides in myelin membranes of the nervous system. The UDP-glycosyl transferases share a conserved signature domain of about 50 amino acid residues (PROSITE: PDOC00359, http://expasy.hcuge.ch/sprot/prosite.html).

[0029] Methyl transferases are involved in a variety of pharmacologically important processes. Nicotinamide N-methyl transferase catalyzes the N-methylation of nicotinamides and other pyridines, an important step in the cellular handling of drugs and other foreign compounds. Phenylethanolamine N-methyl transferase catalyzes the conversion of noradrenalin to adrenalin. 6-O-methylguanine-DNA methyl transferase reverses DNA methylation, an important step in carcinogenesis. Uroporphyrin-III C-methyl transferase, which catalyzes the transfer of two methyl groups from S-adenosyl-L-methionine to uroporphyrinogen III, is the first specific enzyme in the biosynthesis of cobalamin, a dietary enzyme whose uptake is deficient in pernicious anemia. Protein-arginine methyl transferases catalyze the posttranslational methylation of arginine residues in proteins, resulting in the mono- and dimethylation of arginine on the guanidino group. Substrates include histones, myelin basic protein, and heterogeneous nuclear ribonucleoproteins involved in mRNA processing, splicing, and transport. Protein-arginine methyl transferase interacts with proteins upregulated by mitogens, with proteins involved in chronic lymphocytic leukemia, and with interferon, suggesting an important role for methylation in cytokine receptor signaling (Lin, W.-J. et al. (1996) J. Biol. Chem. 271:15034-15044; Abramovich, C. et al. (1997) EMBO J. 16:260-266; and Scott, H. S. et al. (1998) Genomics 48:330-340).

[0030] Phosphotransferases catalyze the transfer of high-energy phosphate groups and are important in energy-requiring and -releasing reactions. The metabolic enzyme creatine kinase catalyzes the reversible phosphate transfer between creatine/creatine phosphate and ATP/ADP. Glycocyamine kinase catalyzes phosphate transfer from ATP to guanidoacetate, and arginine kinase catalyzes phosphate transfer from ATP to argenine. A cysteine-containing active site is conserved in this family (PROSITE: PDOC00103).

[0031] Prenyl transferases are heterodimers, consisting of an alpha and a beta subunit, that catalyze the transfer of an isoprenyl group. An example of a prenyl transferase is the mammalian protein farnesyl transferase. The alpha subunit of farnesyl transferase consists of 5 repeats of 34 amino acids each, with each repeat containing an invariant tryptophan (PROSITE: PDOC00703).

[0032] Saccharyl transferases are glycating enzymes involved in a variety of metabolic processes. Oligosacchryl transferase-48, for example, is a receptor for advanced glycation endproducts. Accumulation of these endproducts is observed in vascular complications of diabetes, macrovascular disease, renal insufficiency, and Alzheimer's disease (Thornalley, P. J. (1998) Cell Mol. Biol. (Noisy-Le-Grand) 44:1013-1023).

[0033] Coenzyme A (CoA) transferase catalyzes the transfer of CoA between two carboxylic acids. Succinyl CoA:3-oxoacid CoA transferase, for example, transfers CoA from succinyl-CoA to a recipient such as acetoacetate. Acetoacetate is essential to the metabolism of ketone bodies, which accumulate in tissues affected by metabolic disorders such as diabetes (PROSITE: PDOC00980).

[0034] Hydrolases

[0035] Hydrolysis is the breaking of a covalent bond in a substrate by introduction of a molecule of water. The reaction involves a nucleophilic attack by the water molecule's oxygen atom on a target bond in the substrate. The water molecule is split across the target bond, breaking the bond and generating two product molecules. Hydrolases participate in reactions essential to such functions as synthesis and degradation of cell components, and for regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Hydrolases are involved in key steps in disease processes involving these functions. Hydrolytic enzymes, or hydrolases, may be grouped by substrate specificity into classes including phosphatases, peptidases, lysophospholipases, phosphodiesterases, glycosidases, and glyoxalases.

[0036] Phosphatases hydrolytically remove phosphate groups from proteins, an energy-providing step that regulates many cellular processes, including intracellular signaling pathways that in turn control cell growth and differentiation, cell-cell contact, the cell cycle, and oncogenesis.

[0037] Lysophospholipases (LPLs) regulate intracellular lipids by catalyzing the hydrolysis of ester bonds to remove an acyl group, a key step in lipid degradation. Small LPL isoforms, approximately 15-30 kD, function as hydrolases; larger isoforms function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes. LPL activity is regulated by signaling molecules important in numerous pathways, including the inflammatory response.

[0038] Peptidases, also called proteases, cleave peptide bonds that form the backbone of peptide or protein chains. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Since typical protein half-lives range from hours to a few days, peptidases are continually cleaving precursor proteins to their active form, removing signal sequences from targeted proteins, and degrading aged or defective proteins. Peptidases function in bacterial, parasitic, and viral invasion and replication within a host. Examples of peptidases include trypsin and chymotrypsin (components of the complement cascade and the blood-clotting cascade) lysosomal cathepsins, calpains, pepsin, renin, and chymosin (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 1-5).

[0039] The phosphodiesterases catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound. Phosphodiesterases are therefore crucial to a variety of cellular processes. Phosphodiesterases include DNA and RNA endo- and exo-nucleases, which are essential to cell growth and replication as well as protein synthesis. Another phosphodiesterase is acid sphingomyelinase, which hydrolyzes the membrane phospholipid sphingomyelin to ceramide and phosphorylcholine. Phosphorylcholine is used in the synthesis of phosphatidylcholine, which is involved in numerous intracellular signaling pathways. Ceramide is an essential precursor for the generation of gangliosides, membrane lipids found in high concentration in neural tissue. Defective acid sphingomyelinase phosphodiesterase leads to a build-up of sphingomyelin molecules in lysosomes, resulting in Niemann-Pick disease.

[0040] Glycosidases catalyze the cleavage of hemiacetyl bonds of glycosides, which are compounds that contain one or more sugar. Mammalian lactase-phlorizin hydrolase, for example, is an intestinal enzyme that splits lactose. Mammalian beta-galactosidase removes the terminal galactose from gangliosides, glycoproteins, and glycosaminoglycans, and deficiency of this enzyme is associated with a gangliosidosis known as Morquio disease type B. Vertebrate lysosomal alpha-glucosidase, which hydrolyzes glycogen, maltose, and isomaltose, and vertebrate intestinal sucrase-isomaltase, which hydrolyzes sucrose, maltose, and isomaltose, are widely distributed members of this family with highly conserved sequences at their active sites.

[0041] The glyoxylase system is involved in gluconeogenesis, the production of glucose from storage compounds in the body. It consists of glyoxylase I, which catalyzes the formation of S—D-lactoylglutathione from methyglyoxal, a side product of triose-phosphate energy metabolism, and glyoxylase II, which hydrolyzes S—D-lactoylglutathione to D-lactic acid and reduced glutathione. Glyoxylases are involved in hyperglycemia, non-insulin-dependent diabetes mellitus, the detoxification of bacterial toxins, and in the control of cell proliferation and microtubule assembly.

[0042] Lyases

[0043] Lyases are a class of enzymes that catalyze the cleavage of C—C, C—O, C—N, C—S, C-(halide), P—O or other bonds without hydrolysis or oxidation to form two molecules, at least one of which contains a double bond (Stryer, L. (1995) Biochemistry W. H. Freeman and Co. New York, N.Y. p.620). Lyases are critical components of cellular biochemistry with roles in metabolic energy production including fatty acid metabolism, as well as other diverse enzymatic processes. Further classification of lyases reflects the type of bond cleaved as well as the nature of the cleaved group.

[0044] The group of C—C lyases include carboxyl-lyases (decarboxylases), aldehyde-lyases (aldolases), oxo-acid-lyases and others. The C—O lyase group includes hydro-lyases, lyases acting on polysaccharides and other lyases. The C—N lyase group includes ammonia-lyases, amidine-lyases, amine-lyases (deaminases) and other lyases.

[0045] Proper regulation of lyases is critical to normal physiology. For example, mutation induced deficiencies in the uroporphyrinogen decarboxylase can lead to photosensitive cutaneous lesions in the genetically-linked disorder familial porphyria cutanea tarda (Mendez, M. et al. (1998) Am. J. Genet. 63:1363-1375). It has also been shown that adenosine deaminase (ADA) deficiency stems from genetic mutations in the ADA gene, resulting in the disorder severe combined immunodeficiency disease (SCID) (Hershfield, M. S. (1998) Semin. Hematol. 35:291-298).

[0046] Isomerases

[0047] Isomerases are a class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. This class includes racemases and epimerases, cis-trans-isomerases, intramolecular oxidoreductases, -intramolecular transferases (mutases) and intramolecular lyases. Isomerases are critical components of cellular biochemistry with roles in metabolic energy production including glycolysis, as well as other diverse enzymatic processes (Stryer, L. (1995) Biochemistry, W. H. Freeman and Co., New York N.Y., pp.483-507).

[0048] Racemases are a subset of isomerases that catalyze inversion of a molecules configuration around the asymmetric carbon atom in a substrate having a single center of asymmetry, thereby interconverting two racemers. Epimerases are another subset of isomerases that catalyze inversion of configuration around an asymmetric carbon atom in a substrate with more than one center of symmetry, thereby interconverting two epimers. Racemases and epimerases can act on amino acids and derivatives, hydroxy acids and derivatives, as well as carbohydrates and derivatives. The interconversion of UDP-galactose and UDP-glucose is catalyzed by UDP-galactose-4′-epimerase. Proper regulation and function of this epimerase is essential to the synthesis of glycoproteins and glycolipids. Elevated blood galactose levels have been correlated with UDP-galactose-4′-epimerase deficiency in screening programs of infants (Gitzelmann, R. (1972) Helv. Paediat. Acta 27:125-130).

[0049] Oxidoreductases can be isomerases as well. Oxidoreductases catalyze the reversible transfer of electrons from a substrate that becomes oxidized to a substrate that becomes reduced. This class of enzymes includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases. Proper maintenance of oxidoreductase levels is physiologically important. For example, genetically-linked deficiencies in lipoamide dehydrogenase can result in lactic acidosis (Robinson, B. H. et al. (1977) Pediat. Res. 11:1198-1202).

[0050] Another subgroup of isomerases are the transferases (or mutases). Transferases transfer a chemical group from one compound (the donor) to another compound (the acceptor). The types of groups transferred by these enzymes include acyl groups, amino groups, phosphate groups (phosphotransferases or phosphomutases), and others. The transferase carnitine palmitoyltransferase is an important component of fatty acid metabolism. Genetically-linked deficiencies in this transferase can lead to myopathy (Scriver, C. R. et al. (1995) The Metabolic and Molecular Basis of Inherited Disease, McGraw-Hill, New York N.Y., pp.1501-1533).

[0051] Yet another subgroup of isomerases are the topoisomersases. Topoisomerases are enzymes that affect the topological state of DNA. For example, defects in topoisomerases or their regulation can affect normal physiology. Reduced levels of topoisomerase II have been correlated with some of the DNA processing defects associated with the disorder ataxia-telangiectasia (Singh, S. P. et al. (1988) Nucleic Acids Res. 16:3919-3929).

[0052] Ligases

[0053] Ligases catalyze the formation of a bond between two substrate molecules. The process involves the hydrolysis of a pyrophosphate bond in ATP or a similar energy donor. Ligases are classified based on the nature of the type of bond they form, which can include carbon-oxygen, carbon-sulfur, carbon-nitrogen, carbon-carbon and phosphoric ester bonds.

[0054] Ligases forming carbon-oxygen bonds include the aminoacyl-transfer RNA (tRNA) synthetases which are important RNA-associated enzymes with roles in translation. Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, and each class is characterized by a distinctive topology of the catalytic domain. Class I enzymes contain a catalytic domain based on the nucleotide-binding Rossman fold. Class II enzymes contain a central catalytic domain, which consists of a seven-stranded antiparallel β-sheet motif, as well as N- and C- terminal regulatory domains. Class II enzymes are separated into two groups based on the heterodimeric or homodimeric structure of the enzyme; the latter group is further subdivided by the structure of the N- and C-terminal regulatory domains (Hartlein, M. and S. Cusack (1995) J. Mol. Evol. 40:519-530). Autoantibodies against aminoacyl-tRNAs are generated by patients with dennatomyositis and polymyositis, and correlate strongly with complicating interstitial lung disease (ILD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals.

[0055] Ligases forming carbon-sulfur bonds (Acid-thiol ligases) mediate a large number of cellular biosynthetic intermediary metabolism processes involve intermolecular transfer of carbon atom-containing substrates (carbon substrates). Examples of such reactions include the tricarboxylic acid cycle, synthesis of fatty acids and long-chain phospholipids, synthesis of alcohols and aldehydes, synthesis of intermediary metabolites, and reactions involved in the amino acid degradation pathways. Some of these reactions require input of energy, usually in the form of conversion of ATP to either ADP or AMP and pyrophosphate.

[0056] In many cases, a carbon substrate is derived from a small molecule containing at least two carbon atoms. The carbon substrate is often covalently bound to a larger molecule which acts as a carbon substrate carrier molecule within the cell. In the biosynthetic mechanisms described above, the carrier molecule is coenzyme A. Coenzyme A (CoA) is structurally related to derivatives of the nucleotide ADP and consists of 4′-phosphopantetheine linked via a phosphodiester bond to the alpha phosphate group of adenosine 3′, 5′-bisphosphate. The terminal thiol group of 4′-phosphopantetheine acts as the site for carbon substrate bond formation. The predominant carbon substrates which utilize CoA as a carrier molecule during biosynthesis and intermediary metabolism in the cell are acetyl, succinyl, and propionyl moieties, collectively referred to as acyl groups. Other carbon substrates include enoyl lipid, which acts as a fatty acid oxidation intermediate, and carnitine, which acts as an acetyl-CoA flux regulator/mitochondrial acyl group transfer protein. Acyl-CoA and acetyl-CoA are synthesized in the cell by acyl-CoA synthetase and acetyl-CoA synthetase, respectively.

[0057] Activation of fatty acids is mediated by at least three forms of acyl-CoA synthetase activity: i) acetyl-CoA synthetase, which activates acetate and several other low molecular weight carboxylic acids and is found in muscle mitochondria and the cytosol of other tissues; ii) medium-chain acyl-CoA synthetase, which activates fatty acids containing between four and eleven carbon atoms (predominantly from dietary sources), and is present only in liver mitochondria; and iii) acyl CoA synthetase, which is specific for long chain fatty acids with between six and twenty carbon atoms, and is found in microsomes and the mitochondria. Proteins associated with acyl-CoA synthetase activity have been identified from many sources including bacteria, yeast, plants, mouse, and man. The activity of acyl-CoA synthetase may be modulated by phosphorylation of the enzyme by cAMP-dependent protein kinase.

[0058] Ligases forming carbon-nitrogen bonds include amide synthases such as glutamine synthetase (glutamate-ammonia ligase) that catalyzes the amination of glutamic acid to glutamine by ammonia using the energy of ATP hydrolysis. Glutamine is the primary source for the amino group in various amide transfer reactions involved in de novo pyrimidine nucleotide synthesis and in purine and pyrimidine ribonucleotide interconversions. Overexpression of glutamine synthetase has been observed in primary liver cancer (Christa, L. et al. (1994) Gastroent. 106:1312-1320).

[0059] Acid-amino-acid ligases (peptide synthases) are represented by the ubiquitin proteases which are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin (Ub), a small heat stable protein. Ub is first activated by a ubiquitin-activating enzyme (El), and then transferred to one of several Ub-conjugating enzymes (E2). E2 then links the Ub molecule through its C-terminal glycine to an internal lysine (acceptor lysine) of a target protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183).

[0060] Cyclo-ligases and other carbon-nitrogen ligases comprise various enzymes and enzyme complexes that participate in the de novo pathways to purine and pyrimidine biosynthesis. Because these pathways are critical to the synthesis of nucleotides for replication of both RNA and DNA, many of these enzymes have been the targets of clinical agents for the treatment of cell proliferative disorders such as cancer and infectious diseases.

[0061] Purine biosynthesis occurs de novo from the amino acids glycine and glutamine, and other small molecules. Three of the key reactions in this process are catalyzed by a trifunctional enzyme composed of glycinamide-ribonucleotide synthetase (GARS), aminoimidazole ribonucleotide synthetase (AIRS), and glycinamide ribonucleotide transformylase (GART). Together these three enzymes combine ribosylamine phosphate with glycine to yield phosphoribosyl aminoimidazole, a precursor to both adenylate and guanylate nucleotides. This trifunctional protein has been implicated in the pathology of Downs syndrome (Aimi, J. et al. (1990) Nucleic Acid Res. 18:6665-6672). Adenylosuccinate synthetase catalyzes a later step in purine biosynthesis that converts inosinic acid to adenylosuccinate, a key step on the path to ATP synthesis. This enzyme is also similar to another carbon-nitrogen ligase, argininosuccinate synthetase, that catalyzes a similar reaction in the urea cycle (Powell, S. M. et al. (1992) FEBS Lett. 303:4-10).

[0062] Like the de novo biosynthesis of purines, de novo synthesis of the pyrimidine nucleotides uridylate and cytidylate also arises from a common precursor, in this instance the nucleotide orotidylate derived from orotate and phosphoribosyl pyrophosphate (PPRP). Again a trifunctional enzyme comprising three carbon-nitrogen ligases plays a key role in the process. In this case the enzymes aspartate transcarbamylase (ATCase), carbamyl phosphate synthetase II, and dihydroorotase (DHOase) are encoded by a single gene called CAD. Together these three enzymes combine the initial reactants in pyrimidine biosynthesis, glutamine, CO₂, and ATP to form dihydroorotate, the precursor to orotate and orotidylate (Iwahana, H. et al. (1996) Biochem. Biophys. Res. Commun. 219:249-255). Further steps then lead to the synthesis of uridine nucleotides from orotidylate. Cytidine nucleotides are derived from uridine-5′-triphosphate (UTP) by the amidation of UTP using glutamine as the amino donor and the enzyme CTP synthetase. Regulatory mutations in the human CTP synthetase are believed to confer multi-drug resistance to agents widely used in cancer therapy (Yamauchi, M. et al. (1990) EMBO J. 9:2095-2099).

[0063] Ligases forming carbon-carbon bonds include the carboxylases acetyl-CoA carboxylase and pyruvate carboxylase. Acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA from CO₂ and H₂O using the energy of ATP hydrolysis. Acetyl-CoA carboxylase is the rate-limiting step in the biogenesis of long-chain fatty acids. Two isoforms of acetyl-CoA carboxylase, types I and types II, are expressed in human in a tissue-specific manner (Ha, J. et al. (1994) Eur. J. Biochem. 219:297-306). Pyruvate carboxylase is a nuclear-encoded mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate, a key intermediate in the citric acid cycle.

[0064] Ligases forming phosphoric ester bonds include the DNA ligases involved in both DNA replication and repair. DNA ligases seal phosphodiester bonds between two adjacent nucleotides in a DNA chain using the energy from ATP hydrolysis to first activate the free 5′-phosphate of one nucleotide and then react it with the 3′-OH group of the adjacent nucleotide. This resealing reaction is used in both DNA replication to join small DNA fragments called Okazaki fragments that are transiently formed in the process of replicating new DNA, and in DNA repair. DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA, are corrected before replication or transcription of the DNA can occur. Bloom's syndrome is an inherited human disease in which individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., p. 247).

[0065] Molecules Associated with Growth and Development

[0066] SEQ ID NO:51 and SEQ ID NO:52 encode, for example, molecules associated with growth and development.

[0067] Human growth and development requires the spatial and temporal regulation of cell differentiation, cell proliferation, and apoptosis. These processes coordinately control reproduction, aging, embryogenesis, morphogenesis, organogenesis, and tissue repair and maintenance. At the cellular level, growth and development is governed by the cell's decision to enter into or exit from the cell division cycle and by the cell's commitment to a terminally differentiated state. These decisions are made by the cell in response to extracellular signals and other environmental cues it receives. The following discussion focuses on the molecular mechanisms of cell division, reproduction, cell differentiation and proliferation, apoptosis, and aging.

[0068] Cell Division

[0069] Cell division is the fundamental process by which all living things grow and reproduce. In unicellular organisms such as yeast and bacteria, each cell division doubles the number of organisms, while in multicellular species many rounds of cell division are required to replace cells lost by wear or by programmed cell death, and for cell differentiation to produce a new tissue or organ. Details of the cell division cycle may vary, but the basic process consists of three principle events. The first event, interphase, involves preparations for cell division, replication of the DNA, and production of essential proteins. In the second event, mitosis, the nuclear material is divided and separates to opposite sides of the cell. The final event, cytokinesis, is division and fission of the cell cytoplasm. The sequence and timing of cell cycle transitions is under the control of the cell cycle regulation system which controls the process by positive or negative regulatory circuits at various check points.

[0070] Regulated progression of the cell cycle depends on the integration of growth control pathways with the basic cell cycle machinery. Cell cycle regulators have been identified by selecting for human and yeast cDNAs that block or activate cell cycle arrest signals in the yeast mating pheromone pathway when they are overexpressed. Known regulators include human CPR (cell cycle progression restoration) genes, such as CPR8 and CPR2, and yeast CDC (cell division control) genes, including CDC91, that block the arrest signals. The CPR genes express a variety of proteins including cyclins, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M. C. et al.(1997) Genetics 147:1063-1076).

[0071] Several cell cycle transitions, including the entry and exit of a cell from mitosis, are dependent upon the activation and inhibition of cyclin-dependent kinases (Cdks). The Cdks are composed of a kinase subunit, Cdk, and an activating subunit, cyclin, in a complex that is subject to many levels of regulation. There appears to be a single Cdk in Saccharomyces cerevisiae and Saccharomyces pombe whereas mammals have a variety of specialized Cdks. Cyclins act by binding to and activating cyclin-dependent protein kinases which then phosphorylate and activate selected proteins involved in the mitotic process. The Cdk-cyclin complex is both positively and negatively regulated by phosphorylation, and by targeted degradation involving molecules such as CDC4 and CDC53. In addition, Cdks are further regulated by binding to inhibitors and other proteins such as Suc 1 that modify their specificity or accessibility to regulators (Patra, D. and W. G. Dunphy (1996) Genes Dev. 10:1503-1515; and Mathias, N. et al. (1996) Mol. Cell Biol. 16:6634-6643).

[0072] Reproduction

[0073] The male and female reproductive systems are complex and involve many aspects of growth and development. The anatomy and physiology of the male and female reproductive systems are reviewed in (Guyton, A. C. (1991) Textbook of Medical Physiology, W. B. Saunders Co., Philadelphia Pa., pp. 899-928).

[0074] The male reproductive system includes the process of spermatogenesis, in which the sperm are formed, and male reproductive functions are regulated by various hormones and their effects on accessory sexual organs, cellular metabolism, growth, and other bodily functions.

[0075] Spermatogenesis begins at puberty as a result of stimulation by gonadotropic hormones released from the anterior pituitary. Immature sperm (spermatogonia) undergo several mitotic cell divisions before undergoing meiosis and full maturation. The testes secrete several male sex hormones, the most abundant being testosterone, that is essential for growth and division of the immature sperm, and for the masculine characteristics of the male body. Three other male sex hormones, gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) control sexual function.

[0076] The uterus, ovaries, fallopian tubes, vagina, and breasts comprise the female reproductive system. The ovaries and uterus are the source of ova and the location of fetal development, respectively. The fallopian tubes and vagina are accessory organs attached to the top and bottom of the uterus, respectively. Both the uterus and ovaries have additional roles in the development and loss of reproductive capability during a female's lifetime. The primary role of the breasts is lactation. Multiple endocrine signals from the ovaries, uterus, pituitary, hypothalamus, adrenal glands, and other tissues coordinate reproduction and lactation. These signals vary during the monthly menstruation cycle and during the female's lifetime. Similarly, the sensitivity of reproductive organs to these endocrine signals varies during the female's lifetime.

[0077] A combination of positive and negative feedback to the ovaries, pituitary and hypothalamus glands controls physiologic changes during the monthly ovulation and endometrial cycles. The anterior pituitary secretes two major gonadotropin hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regulated by negative feedback of steroids, most notably by ovarian estradiol. If fertilization does not occur, estrogen and progesterone levels decrease. This sudden reduction of the ovarian hormones leads to menstruation, the desquamation of the endometrium.

[0078] Hormones further govern all the steps of pregnancy, parturition, lactation, and menopause. During pregnancy large quantities of human chorionic gonadotropin (hCG), estrogens, progesterone, and human chorionic somatomammotropin (hCS) are formed by the placenta. hCG, a glycoprotein similar to luteinizing hormone, stimulates the corpus luteum to continue producing more progesterone and estrogens, rather than to involute as occurs if the ovum is not fertilized. hCS is similar to growth hormone and is crucial for fetal nutrition.

[0079] The female breast also matures during pregnancy. Large amounts of estrogen secreted by the placenta trigger growth and branching of the breast milk ductal system while lactation is initiated by the secretion of prolactin by the pituitary gland.

[0080] Parturition involves several hormonal changes that increase uterine contractility toward the end of pregnancy, as follows. The levels of estrogens increase more than those of progesterone. Oxytocin is secreted by the neurohypophysis. Concomitantly, uterine sensitivity to oxytocin increases. The fetus itself secretes oxytocin, cortisol (from adrenal glands), and prostaglandins.

[0081] Menopause occurs when most of the ovarian follicles have degenerated. The ovary then produces less estradiol, reducing the negative feedback on the pituitary and hypothalamus glands. Mean levels of circulating FSH and LH increase, even as ovulatory cycles continue. Therefore, the ovary is less responsive to gonadotropins, and there is an increase in the time between menstrual cycles. Consequently, menstrual bleeding ceases and reproductive capability ends.

[0082] Cell Differentiation and Proliferation

[0083] Tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.

[0084] Growth factors were originally described as serum factors required to promote cell proliferation. Most growth factors are large, secreted polypeptides that act on cells in their local environment. Growth factors bind to and activate specific cell surface receptors and initiate intracellular signal transduction cascades. Many growth factor receptors are classified as receptor tyrosine kinases which undergo autophosphorylation upon ligand binding. Autophosphorylation enables the receptor to interact with signal transduction proteins characterized by the presence of SH2 or SH3 domains (Src homology regions 2 or 3). These proteins then modulate the activity state of small G-proteins, such as Ras, Rab, and Rho, along with GTPase activating proteins (GAPs), guanine nucleotide releasing proteins (GNRPs), and other guanine nucleotide exchange factors. Small G proteins act as molecular switches that activate other downstream events, such as mitogen-activated protein kinase (MAP kinase) cascades. MAP kinases ultimately activate transcription of mitosis-promoting genes.

[0085] In addition to growth factors, small signaling peptides and hormones also influence cell proliferation. These molecules bind primarily to another class of receptor, the trimeric G-protein-coupled receptor (GPCR), found predominantly on the surface of immune, neuronal and neuroendocrine cells. Upon ligand binding, the GPCR activates a trimeric G protein which in turn triggers increased levels of intracellular second messengers such as phospholipase C, Ca2+, and cyclic AMP. Most GPCR-mediated signaling pathways indirectly promote cell proliferation by causing the secretion or breakdown of other signaling molecules that have direct mitogenic effects. These signaling cascades often involve activation of kinases and phosphatases. Some growth factors, such as some members of the transforming growth factor beta (TGF-β) family, act on some cells to stimulate cell proliferation and on other cells to inhibit it. Growth factors may also stimulate a cell at one concentration and inhibit the same cell at another concentration. Most growth factors also have a multitude of other actions besides the regulation of cell growth and division: they can control the proliferation, survival, differentiation, migration, or function of cells depending on the circumstance. For example, the tumor necrosis factor/nerve growth factor (TNF/NGF) family can activate or inhibit cell death, as well as regulate proliferation and differentiation. The cell response depends on the type of cell, its stage of differentiation and transformation status, which surface receptors are stimulated, and the types of stimuli acting on the cell (Smith, A. et al. (1994) Cell 76:959-962; and Nocentini, G. et al. (1997) Proc. Natl. Acad. Sci. USA 94:6216-6221).

[0086] Neighboring cells in a tissue compete for growth factors, and when provided with “unlimited” quantities in a perfused system will grow to even higher cell densities before reaching density-dependent inhibition of cell division. Cells often demonstrate an anchorage dependence of cell division as well. This anchorage dependence may be associated with the formation of focal contacts linking the cytoskeleton with the extracellular matrix (ECM). The expression of ECM components can be stimulated by growth factors. For example, TGF-β stimulates fibroblasts to produce a variety of ECM proteins, including fibronectin, collagen, and tenascin (Pearson, C. A. et al. (1988) EMBO J. 7:2677-2981). In fact, for some cell types specific ECM molecules, such as laminin or fibronectin, may act as growth factors. Tenascin-C and -R, expressed in developing and lesioned neural tissue, provide stimulatory/anti-adhesive or inhibitory properties, respectively, for axonal growth (Faissner, A. (1997) Cell Tissue Res. 290:331-341).

[0087] Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which convert normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression. The latter category of oncoprotein causes cancer by altering transcriptional control of cell proliferation. Five classes of oncoproteins are known to affect cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps.

[0088] Many oncogenes have been identified and characterized. These include sis, erbA, erbB, her-2, mutated G_(s), src, abl, ras, crk, jun, fos, myc, and mutated tumor-suppressor genes such as RB, p53, mdm2, Cip1, p16, and cyclin D. Transformation of normal genes to oncogenes may also occur by chromosomal translocation. The Philadelphia chromosome, characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22.

[0089] Tumor-suppressor genes are involved in regulating cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proliferation. For example, the retinoblastoma gene product (RB), in a non-phosphorylated state, binds several early-response genes and suppresses their transcription, thus blocking cell division. Phosphorylation of RB causes it to dissociate from the genes, releasing the suppression, and allowing cell division to proceed.

[0090] Apoptosis

[0091] Apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Selective elimination of cells is as important for morphogenesis and tissue remodeling as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proliferation. Apoptosis is also a critical component of the immune response. Immune cells such as cytotoxic T-cells and natural killer cells prevent the spread of disease by inducing apoptosis in tumor cells and virus-infected cells. In addition, immune cells that fail to distinguish self molecules from foreign molecules must be eliminated by apoptosis to avoid an autoimmune response.

[0092] Apoptotic cells undergo distinct morphological changes. Hallmarks of apoptosis include cell shrinkage, nuclear and cytoplasmic condensation, and alterations in plasma membrane topology. Biochemically, apoptotic cells are characterized by increased intracellular calcium concentration, fragmentation of chromosomal DNA, and expression of novel cell surface components.

[0093] The molecular mechanisms of apoptosis are highly conserved, and many of the key protein regulators and effectors of apoptosis have been identified. Apoptosis generally proceeds in response to a signal which is transduced intracellularly and results in altered patterns of gene expression and protein activity. Signaling molecules such as hormones and cytokines are known both to stimulate and to inhibit apoptosis through interactions with cell surface receptors. Transcription factors also play an important role in the onset of apoptosis. A number of downstream effector molecules, particularly proteases such as the cysteine proteases called caspases, have been implicated in the degradation of cellular components and the proteolytic activation of other apoptotic effectors.

[0094] Aging and Senescence

[0095] Studies of the aging process or senescence have shown a number of characteristic cellular and molecular changes (Fauci et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., p.37). These characteristics include increases in chromosome structural abnormalities, DNA cross-linking, incidence of single-stranded breaks in DNA, losses in DNA methylation, and degradation of telomere regions. In addition to these DNA changes, post-translational alterations of proteins increase including, deamidation, oxidation, cross-linking, and nonenzymatic glycation. Still further molecular changes occur in the mitochondria of aging cells through deterioration of structure. These changes eventually contribute to decreased function in every organ of the body.

[0096] Biochemical Pathway Molecules

[0097] SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, and SEQ ID NO:50 encode, for example, biochemical pathway molecules.

[0098] Biochemical pathways are responsible for regulating metabolism, growth and development, protein secretion and trafficking, environmental responses, and ecological interactions including immune response and response to parasites.

[0099] DNA replication

[0100] Deoxyribonucleic acid (DNA), the genetic material, is found in both the nucleus and mitochondria of human cells. The bulk of human DNA is nuclear, in the form of linear chromosomes, while mitochondrial DNA is circular. DNA replication begins at specific sites called origins of replication. Bidirectional synthesis occurs from the origin via two growing forks that move in opposite directions. Replication is semi-conservative, with each daughter duplex containing one old strand and its newly synthesized complementary partner. Proteins involved in DNA replication include DNA polymerases, DNA primase, telomerase, DNA helicase, topoisomerases, DNA ligases, replication factors, and DNA-binding proteins.

[0101] DNA Recombination and Repair

[0102] Cells are constantly faced with replication errors and environmental assault (such as ultraviolet irradiation) that can produce DNA damage. Damage to DNA consists of any change that modifies the structure of the molecule. Changes to DNA can be divided into two general classes, single base changes and structural distortions. Any damage to DNA can produce a mutation, and the mutation may produce a disorder, such as cancer.

[0103] Changes in DNA are recognized by repair systems within the cell. These repair systems act to correct the damage and thus prevent any deleterious affects of a mutational event. Repair systems can be divided into three general types, direct repair, excision repair, and retrieval systems. Proteins involved in DNA repair include DNA polymerase, excision repair proteins, excision and cross link repair proteins, recombination and repair proteins, RAD51 proteins, and BLN and WRN proteins that are homologs of RecQ helicase. When the repair systems are eliminated, cells become exceedingly sensitive to environmental mutagens, such as ultraviolet irradiation. Patients with disorders associated with a loss in DNA repair systems often exhibit a high sensitivity to environmental mutagens. Examples of such disorders include xeroderma pigmentosum (XP), Bloom's syndrome (BS), and Werner's syndrome (WS) (Yamagata, K. et al. (1998) Proc. Natl. Acad. Sci. USA 95:8733-8738), ataxia telangiectasia, Cockayne's syndrome, and Fanconi's anemia.

[0104] Recombination is the process whereby new DNA sequences are generated by the movements of large pieces of DNA. In homologous recombination, which occurs during meiosis and DNA repair, parent DNA duplexes align at regions of sequence similarity, and new DNA molecules form by the breakage and joining of homologous segments. Proteins involved include RAD51 recombinase. In site-specific recombination, two specific but not necessarily homologous DNA sequences are exchanged. In the immune system this process generates a diverse collection of antibody and T cell receptor genes. Proteins involved in site-specific recombination in the immune system include recombination activating genes 1 and 2 (RAG1 and RAG2). A defect in immune system site-specific recombination causes severe combined immunodeficiency disease in mice.

[0105] RNA Metabolism

[0106] Ribonucleic acid (RNA) is a linear single-stranded polymer of four nucleotides, ATP, CTP, UTP, and GTP. In most organisms, RNA is transcribed as a copy of DNA, the genetic material of the organism. In retroviruses RNA rather than DNA serves as the genetic material. RNA copies of the genetic material encode proteins or serve various structural, catalytic, or regulatory roles in organisms. RNA is classified according to its cellular localization and function. Messenger RNAs (mRNAs) encode polypeptides. Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate mRNA into polypeptides. Transfer RNAs (tRNAs) are cytosolic adaptor molecules that function in mRNA translation by recognizing both an mRNA codon and the amino acid that matches that codon. Heterogeneous nuclear RNAs (hnRNAs) include mRNA precursors and other nuclear RNAs of various sizes. Small nuclear RNAs (snRNAs) are a part of the nuclear spliceosome complex that removes intervening, non-coding sequences (introns) and rejoins exons in pre-mRNAs.

[0107] RNA Transcription

[0108] The transcription process synthesizes an RNA copy of DNA. Proteins involved include multi-subunit RNA polymerases, transcription factors IIA, IIB, IID, IIE, IIF, IIH, and IIJ. Many transcription factors incorporate DNA-binding structural motifs which comprise either α-helices or β-sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix.

[0109] RNA Processing

[0110] Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5′ end with methylguanosine, polyadenylating the 3′ end, and splicing to remove introns. The spliceosomal complex is comprised of five small nuclear ribonucleoprotein particles (snRNPs) designated U1, U2, U4, U5, and U6. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base-pair with intron consensus sequences. The protein components mediate spliceosome assembly and the splicing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry W. H. Freeman and Company, New York N.Y., p. 863).

[0111] Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been identified that have roles in splicing, exporting of the mature RNAs to the cytoplasm, and mRNA translation (Biamonti, G. et al. (1998) Clin. Exp. Rheumatol. 16:317-326). Some examples of hnRNPs include the yeast proteins Hrp1p, involved in cleavage and polyadenylation at the 3′ end of the RNA; Cbp80p, involved in capping the 5′ end of the RNA; and Np13p, a homolog of mammalian hnRNP A1, involved in export of mRNA from the nucleus (Shen, E. C. et al. (1998) Genes Dev. 12:679-691). HnRNPs have been shown to be important targets of the autoimmune response in rheumatic diseases (Biamonti, supra).

[0112] Many snRNP proteins, hnRNP proteins, and alternative splicing factors are characterized by an RNA recognition motif (RRM). (Reviewed in Birney, E. et al. (1993) Nucleic Acids Res. 21:5803-5816.) The RRM is about 80 amino acids in length and forms four Pβ-strands and two α-helices arranged in an α/β sandwich. The RRM contains a core RNP-1 octapeptide motif along with surrounding conserved sequences.

[0113] RNA Stability and Degradation

[0114] RNA helicases alter and regulate RNA conformation and secondary structure by using energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis. (Reviewed in Linder, P. et al. (1989) Nature 337:121-122.)

[0115] Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblastoma (Nb) and retinoblastoma (Rb) tumors. Other DEAD-box helicases have been implicated either directly or indirectly in ultraviolet light-induced tumors, B cell lymphoma, and myeloid malignancies. (Reviewed in Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168.)

[0116] Ribonucleases (RNases) catalyze the hydrolysis of phosphodiester bonds in RNA chains, thus cleaving the RNA. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5′ end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral replication cycle. RNase H domains are often found as a domain associated with reverse transcriptases. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, C. H. (1997) Nat. Biotechnol. 15:529-536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections.

[0117] Protein Translation

[0118] The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Three important sites are identified on the ribosome. The aminoacyl-tRNA site (A site) is where charged tRNAs (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (Translation is reviewed in Stryer, L. (1995) Biochemistry, W. H. Freeman and Company, New York N.Y., pp. 875-908; and Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 119-138.)

[0119] tRNA Charging

[0120] Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, Class I and Class II. Autoantibodies against aminoacyl-tRNAs are generated by patients with dermatomyositis and polymyositis, and correlate strongly with complicating interstitial lung disease (ILD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals.

[0121] Translation Initiation

[0122] Initiation of translation can be divided into three stages. The first stage brings an initiator transfer RNA (Met-tRNAf) together with the 40S ribosomal subunit to form the 43S preinitiation complex. The second stage binds the 43S preinitiation complex to the mRNA, followed by migration of the complex to the correct AUG initiation codon. The third stage brings the 60S ribosomal subunit to the 40S subunit to generate an 80S ribosome at the initiation codon. Regulation of translation primarily involves the first and second stage in the initiation process (Pain, V. M. (1996) Eur. J. Biochem. 236:747-771).

[0123] Several initiation factors, many of which contain multiple subunits, are involved in bringing an initiator tRNA and 40S ribosomal subunit together. eIF2, a guanine nucleotide binding protein, recruits the initiator tRNA to the 40S ribosomal subunit. Only when eIF2 is bound to GTP does it associate with the initiator tRNA. eIF2B, a guanine nucleotide exchange protein, is responsible for converting eIF2 from the GDP-bound inactive form to the GTP-bound active form. Two other factors, eIF1A and eIF3 bind and stabilize the 40S subunit by interacting with 18S ribosomal RNA and specific ribosomal structural proteins. eIF3 is also involved in association of the 40S ribosomal subunit with mRNA. The Met-tRNA_(f), eIF1A, eIF3, and 40S ribosomal subunit together make up the 43S preinitiation complex (Pain, supra).

[0124] Additional factors are required for binding of the 43S preinitiation complex to an mRNA molecule, and the process is regulated at several levels. eIF4F is a complex consisting of three proteins: eIF4E, eIF4A, and eIF4G. eIF4E recognizes and binds to the mRNA 5′-terminal m⁷GTP cap, eIF4A is a bidirectional RNA-dependent helicase, and eIF4G is a scaffolding polypeptide. eIF4G has three binding domains. The N-terminal third of eIF4G interacts with eIF4E, the central third interacts with eIF4A, and the C-terminal third interacts with eIF3 bound to the 43S preinitiation complex. Thus, eIF4G acts as a bridge between the 40S ribosomal subunit and the mRNA (Hentze, M. W. (1997) Science 275:500-501).

[0125] The ability of eIF4F to initiate binding of the 43S preinitiation complex is regulated by structural features of the mRNA. The mRNA molecule has an untranslated region (UTR) between the 5′ cap and the AUG start codon. In some mRNAs this region forms secondary structures that impede binding of the 43S preinitiation complex. The helicase activity of eIF4A is thought to function in removing this secondary structure to facilitate binding of the 43S preinitiation complex (Pain, supra).

[0126] Translation Elongation

[0127] Elongation is the process whereby additional amino acids are joined to the initiator methionine to form the complete polypeptide chain. The elongation factors EF1α, EF1βγ, and EF2 are involved in elongating the polypeptide chain following initiation. EF1α is a GTP-binding protein. In EF1α's GTP-bound form, it brings an aminoacyl-tRNA to the ribosome's A site. The amino acid attached to the newly arrived aminoacyl-tRNA forms a peptide bond with the initiator methionine. The GTP on EF1α is hydrolyzed to GDP, and EF1α-GDP dissociates from the ribosome. EF1β γ binds EF1α-GDP and induces the dissociation of GDP from EF1α, allowing EF1α to bind GTP and a new cycle to begin.

[0128] As subsequent aminoacyl-tRNAs are brought to the ribosome, EF-G, another GTP-binding protein, catalyzes the translocation of tRNAs from the A site to the P site and finally to the E site of the ribosome. This allows the processivity of translation.

[0129] Translation Termination

[0130] The release factor eRF carries out termination of translation. eRF recognizes stop codons in the mRNA, leading to the release of the polypeptide chain from the ribosome.

[0131] Post-Translational Pathways

[0132] Proteins may be modified after translation by the addition of phosphate, sugar, prenyl, fatty acid, and other chemical groups. These modifications are often required for proper protein activity. Enzymes involved in post-translational modification include kinases, phosphatases, glycosyltransferases, and prenyltransferases. The conformation of proteins may also be modified after translation by the introduction and rearrangement of disulfide bonds (rearrangement catalyzed by protein disulfide isomerase), the isomerization of proline sidechains by prolyl isomerase, and by interactions with molecular chaperone proteins.

[0133] Proteins may also be cleaved by proteases. Such cleavage may result in activation, inactivation, or complete degradation of the protein. Proteases include serine proteases, cysteine proteases, aspartic proteases, and metalloproteases. Signal peptidase in the endoplasmic reticulum (ER) lumen cleaves the signal peptide from membrane or secretory proteins that are imported into the ER. Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. Proteins involved in the UCS include ubiquitin-activating enzyme, ubiquitin-conjugating enzymes, ubiquitin-ligases, and ubiquitin C-terminal hydrolases. The ubiquitinated protein is then recognized and degraded by the proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease.

[0134] Lipid Metabolism

[0135] Lipids are water-insoluble, oily or greasy substances that are soluble in nonpolar solvents such as chloroform or ether. Neutral fats (triacylglycerols) serve as major fuels and energy stores. Polar lipids, such as phospholipids, sphingolipids, glycolipids, and cholesterol, are key structural components of cell membranes.

[0136] Lipid metabolism is involved in human diseases and disorders. In the arterial disease atherosclerosis, fatty lesions form on the inside of the arterial wall. These lesions promote the loss of arterial flexibility and the formation of blood clots (Guyton, A. C. Textbook of Medical Physiology (1991) W. B. Saunders Company, Philadelphia Pa., pp.760-763). In Tay-Sachs disease, the GM₂ ganglioside (a sphingolipid) accumulates in lysosomes of the central nervous system due to a lack of the enzyme N-acetylhexosaminidase. Patients suffer nervous system degeneration leading to early death (Fauci, A. S. et al. (1998) Harrison's Principles of Internal Medicine McGraw-Hill, New York N.Y., p. 2171). The Niemann-Pick diseases are caused by defects in lipid metabolism. Niemann-Pick diseases types A and B are caused by accumulation of sphingomyelin (a sphingolipid) and other lipids in the central nervous system due to a defect in the enzyme sphingomyelinase, leading to neurodegeneration and lung disease. Niemann-Pick disease type C results from a defect in cholesterol transport, leading to the accumulation of sphingomyelin and cholesterol in lysosomes and a secondary reduction in sphingomyelinase activity. Neurological symptoms such as grand mal seizures, ataxia, and loss of previously learned speech, manifest 1-2 years after birth. A mutation in the NPC protein, which contains a putative cholesterol-sensing domain, was found in a mouse model of Niemann-Pick disease type C (Fauci, supra, p. 2175; Loftus, S. K. et al. (1997) Science 277:232-235). (Lipid metabolism is reviewed in Stryer, L. (1995) Biochemistry, W. H. Freeman and Company, New York N.Y.; Lehninger, A. (1982) Principles of Biochemistry Worth Publishers, Inc., New York N.Y.; and ExPASy “Biochemical Pathways” index of Boehringer Mannheim World Wide Web site.)

[0137] Fatty Acid Synthesis

[0138] Fatty acids are long-chain organic acids with a single carboxyl group and a long non-polar hydrocarbon tail. Long-chain fatty acids are essential components of glycolipids, phospholipids, and cholesterol, which are building blocks for biological membranes, and of triglycerides, which are biological fuel molecules. Long-chain fatty acids are also substrates for eicosanoid production, and are important in the functional modification of certain complex carbohydrates and proteins. 16-carbon and 18-carbon fatty acids are the most common.

[0139] Fatty acid synthesis occurs in the cytoplasm. In the first step, acetyl-Coenzyme A (CoA) carboxylase (ACC) synthesizes malonyl-CoA from acetyl-CoA and bicarbonate. The enzymes which catalyze the remaining reactions are covalently linked into a single polypeptide chain, referred to as the multifunctional enzyme fatty acid synthase (FAS). FAS catalyzes the synthesis of palmitate from acetyl-CoA and malonyl-CoA. FAS contains acetyl transferase, malonyl transferase, β-ketoacetyl synthase, acyl carrier protein, β-ketoacyl reductase, dehydratase, enoyl reductase, and thioesterase activities. The final product of the FAS reaction is the 16-carbon fatty acid palmitate. Further elongation, as well as unsaturation, of palmitate by accessory enzymes of the ER produces the variety of long chain fatty acids required by the individual cell. These enzymes include a NADH-cytochrome b₅ reductase, cytochrome b₅, and a desaturase.

[0140] Phospholipid and Triacylglycerol Synthesis

[0141] Triacylglycerols, also known as triglycerides and neutral fats, are major energy stores in animals. Triacylglycerols are esters of glycerol with three fatty acid chains. Glycerol-3-phosphate is produced from dihydroxyacetone phosphate by the enzyme glycerol phosphate dehydrogenase or from glycerol by glycerol kinase. Fatty acid-CoA's are produced from fatty acids by fatty acyl-CoA synthetases. Glyercol-3-phosphate is acylated with two fatty acyl-CoA's by the enzyme glycerol phosphate acyltransferase to give phosphatidate. Phosphatidate phosphatase converts phosphatidate to diacylglycerol, which is subsequently acylated to a triacylglyercol by the enzyme diglyceride acyltransferase. Phosphatidate phosphatase and diglyceride acyltransferase form a triacylglyerol synthetase complex bound to the ER membrane.

[0142] A major class of phospholipids are the phosphoglycerides, which are composed of a glycerol backbone, two fatty acid chains, and a phosphorylated alcohol. Phosphoglycerides are components of cell membranes. Principal phosphoglycerides are phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine, phosphatidyl inositol, and diphosphatidyl glycerol. Many enzymes involved in phosphoglyceride synthesis are associated with membranes (Meyers, R. A. (1995) Molecular Biology and Biotechnology, VCH Publishers Inc., New York N.Y., pp. 494-501). Phosphatidate is converted to CDP-diacylglycerol by the enzyme phosphatidate cytidylyltransferase (ExPASy ENZYME EC 2.7.7.41). Transfer of the diacylglycerol group from CDP-diacylglycerol to serine to yield phosphatidyl serine, or to inositol to yield phosphatidyl inositol, is catalyzed by the enzymes CDP-diacylglycerol-serine O-phosphatidyltransferase and CDP-diacylglycerol-inositol 3-phosphatidyltransferase, respectively (ExPASy ENZYME EC 2.7.8.8; ExPASy ENZYME EC 2.7.8.11). The enzyme phosphatidyl serine decarboxylase catalyzes the conversion of phosphatidyl serine to phosphatidyl ethanolamine, using a pyruvate cofactor (Voelker, D. R. (1997) Biochim. Biophys. Acta 1348:236-244). Phosphatidyl choline is formed using diet-derived choline by the reaction of CDP-choline with 1,2-diacylglycerol, catalyzed by diacylglycerol cholinephosphotransferase (ExPASy ENZYME 2.7.8.2).

[0143] Sterol, Steroid, and Isoprenoid Metabolism

[0144] Cholesterol, composed of four fused hydrocarbon rings with an alcohol at one end, moderates the fluidity of membranes in which it is incorporated. In addition, cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, estrogen, and testosterone. Bile salts derived from cholesterol facilitate the digestion of lipids. Cholesterol in the skin forms a barrier that prevents excess water evaporation from the body. Farnesyl and geranylgeranyl groups, which are derived from cholesterol biosynthesis intermediates, are post-translationally added to signal transduction proteins such as ras and protein-targeting proteins such as rab. These modifications are important for the activities of these proteins (Guyton, supra; Stryer, supra, pp. 279-280, 691-702, 934).

[0145] Mammals obtain cholesterol derived from both de novo biosynthesis and the diet. The liver is the major site of cholesterol biosynthesis in mammals. Two acetyl-CoA molecules initially condense to form acetoacetyl-CoA, catalyzed by a thiolase. Acetoacetyl-CoA condenses with a third acetyl-CoA to form hydroxymethylglutaryl-CoA (HMG-CoA), catalyzed by HMG-CoA synthase. Conversion of HMG-CoA to cholesterol is accomplished via a series of enzymatic steps known as the mevalonate pathway. The rate-limiting step is the conversion of HMG-CoA to mevalonate by HMG-CoA reductase. The drug lovastatin, a potent inhibitor of HMG-CoA reductase, is given to patients to reduce their serum cholesterol levels. Other mevalonate pathway enzymes include mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, isopentenyldiphosphate isomerase, dimethylallyl transferase, geranyl transferase, farnesyl-diphosphate farnesyltransferase, squalene monooxygenase, lanosterol synthase, lathosterol oxidase, and 7-dehydrocholesterol reductase.

[0146] Cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, aldosterone, estrogen, and testosterone. First, cholesterol is converted to pregnenolone by cholesterol monooxygenases. The other steroid hormones are synthesized from pregnenolone by a series of enzyme-catalyzed reactions including oxidations, isomerizations, hydroxylations, reductions, and demethylations. Examples of these enzymes include steroid Δ-isomerase, 3β-hydroxy-Δ⁵-steroid dehydrogenase, steroid 21-monooxygenase, steroid 19-hydroxylase, and 3β-hydroxysteroid dehydrogenase. Cholesterol is also the precursor to vitamin D.

[0147] Numerous compounds contain 5-carbon isoprene units derived from the mevalonate pathway intermediate isopentenyl pyrophosphate. Isoprenoid groups are found in vitamin K, ubiquinone, retinal, dolichol phosphate (a carrier of oligosaccharides needed for N-linked glycosylation), and farnesyl and geranylgeranyl groups that modify proteins. Enzymes involved include farnesyl transferase, polyprenyl transferases, dolichyl phosphatase, and dolichyl kinase.

[0148] Sphingolipid Metabolism

[0149] Sphingolipids are an important class of membrane lipids that contain sphingosine, a long chain amino alcohol. They are composed of one long-chain fatty acid, one polar head alcohol, and sphingosine or sphingosine derivative. The three classes of sphingolipids are sphingomyelins, cerebrosides, and gangliosides. Sphingomyelins, which contain phosphocholine or phosphoethanolamine as their head group, are abundant in the myelin sheath surrounding nerve cells. Galactocerebrosides, which contain a glucose or galactose head group, are characteristic of the brain. Other cerebrosides are found in nonneural tissues. Gangliosides, whose head groups contain multiple sugar units, are abundant in the brain, but are also found in nonneural tissues.

[0150] Sphingolipids are built on a sphingosine backbone. Sphingosine is acylated to ceramide by the enzyme sphingosine acetyltransferase. Ceramide and phosphatidyl choline are converted to sphingomyelin by the enzyme ceramide choline phosphotransferase. Cerebrosides are synthesized by the linkage of glucose or galactose to ceramide by a transferase. Sequential addition of sugar residues to ceramide by transferase enzymes yields gangliosides.

[0151] Eicosanoid Metabolism

[0152] Eicosanoids, including prostaglandins, prostacyclin, thromboxanes, and leukotrienes, are 20-carbon molecules derived from fatty acids. Eicosanoids are signaling molecules which have roles in pain, fever, and inflammation. The precursor of all eicosanoids is arachidonate, which is generated from phospholipids by phospholipase A₂ and from diacylglycerols by diacylglycerol lipase. Leukotrienes are produced from arachidonate by the action of lipoxygenases. Prostaglandin synthase, reductases, and isomerases are responsible for the synthesis of the prostaglandins. Prostaglandins have roles in inflammation, blood flow, ion transport, synaptic transmission, and sleep. Prostacyclin and the thromboxanes are derived from a precursor prostaglandin by the action of prostacyclin synthase and thromboxane synthases, respectively.

[0153] Ketone Body Metabolism

[0154] Pairs of acetyl-CoA molecules derived from fatty acid oxidation in the liver can condense to form acetoacetyl-CoA, which subsequently forms acetoacetate, D-3-hydroxybutyrate, and acetone. These three products are known as ketone bodies. Enzymes involved in ketone body metabolism include HMG-CoA synthetase, HMG-CoA cleavage enzyme, D-3-hydroxybutyrate dehydrogenase, acetoacetate decarboxylase, and 3-ketoacyl-CoA transferase. Ketone bodies are a normal fuel supply of the heart and renal cortex. Acetoacetate produced by the liver is transported to cells where the acetoacetate is converted back to acetyl-CoA and enters the citric acid cycle. In times of starvation, ketone bodies produced from stored triacylglyerols become an important fuel source, especially for the brain. Abnormally high levels of ketone bodies are observed in diabetics. Diabetic coma can result if ketone body levels become too great.

[0155] Lipid Mobilization

[0156] Within cells, fatty acids are transported by cytoplasmic fatty acid binding proteins (Online Mendelian Inheritance in Man (OMIM) *134650 Fatty Acid-Binding Protein 1, Liver; FABP1). Diazepam binding inhibitor (DBI), also known as endozepine and acyl CoA-binding protein, is an endogenous γ-aminobutyric acid (GABA) receptor ligand which is thought to down-regulate the effects of GABA. DBI binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters (OMIM *125950 Diazepam Binding Inhibitor; DBI; PROSITE PDOC00686 Acyl-CoA-binding protein signature).

[0157] Fat stored in liver and adipose triglycerides may be released by hydrolysis and transported in the blood. Free fatty acids are transported in the blood by albumin. Triacylglycerols and cholesterol esters in the blood are transported in lipoprotein particles. The particles consist of a core of hydrophobic lipids surrounded by a shell of polar lipids and apolipoproteins. The protein components serve in the solubilization of hydrophobic lipids and also contain cell-targeting signals. Lipoproteins include chylomicrons, chylomicron remnants, very-low-density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL). There is a strong inverse correlation between the levels of plasma HDL and risk of premature coronary heart disease.

[0158] Triacylglycerols in chylomicrons and VLDL are hydrolyzed by lipoprotein lipases that line blood vessels in muscle and other tissues that use fatty acids. Cell surface LDL receptors bind LDL particles which are then internalized by endocytosis. Absence of the LDL receptor, the cause of the disease familial hypercholesterolemia, leads to increased plasma cholesterol levels and ultimately to atherosclerosis. Plasma cholesteryl ester transfer protein mediates the transfer of cholesteryl esters from HDL to apolipoprotein B-containing lipoproteins. Cholesteryl ester transfer protein is important in the reverse cholesterol transport system and may play a role in atherosclerosis (Yamashita, S. et al. (1997) Curr. Opin. Lipidol. 8:101-110). Macrophage scavenger receptors, which bind and internalize modified lipoproteins, play a role in lipid transport and may contribute to atherosclerosis (Greaves, D. R. et al. (1998) Curr. Opin. Lipidol. 9:425-432).

[0159] Proteins involved in cholesterol uptake and biosynthesis are tightly regulated in response to cellular cholesterol levels. The sterol regulatory element binding protein (SREBP) is a sterol-responsive transcription factor. Under normal cholesterol conditions, SREBP resides in the ER membrane. When cholesterol levels are low, a regulated cleavage of SREBP occurs which releases the extracellular domain of the protein. This cleaved domain is then transported to the nucleus where it activates the transcription of the LDL receptor gene, and genes encoding enzymes of cholesterol synthesis, by binding the sterol regulatory element (SRE) upstream of the genes (Yang, J. et al. (1995) J. Biol. Chem. 270:12152-12161). Regulation of cholesterol uptake and biosynthesis also occurs via the oxysterol-binding protein (OSBP). OSBP is a high-affinity intracellular receptor for a variety of oxysterols that down-regulate cholesterol synthesis and stimulate cholesterol esterification (Lagace, T. A. et al. (1997) Biochem. J. 326:205-213).

[0160] Beta-oxidation

[0161] Mitochondrial and peroxisomal beta-oxidation enzymes degrade saturated and unsaturated fatty acids by sequential removal of two-carbon units from CoA-activated fatty acids. The main beta-oxidation pathway degrades both saturated and unsaturated fatty acids while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids.

[0162] The pathways of mitochondrial and peroxisomal beta-oxidation use similar enzymes, but have different substrate specificities and functions. Mitochondria oxidize short-, medium-, and long-chain fatty acids to produce energy for cells. Mitochondrial beta-oxidation is a major energy source for cardiac and skeletal muscle. In liver, it provides ketone bodies to the peripheral circulation when glucose levels are low as in starvation, endurance exercise, and diabetes (Eaton, S. et al. (1996) Biochem. J. 320:345-357). Peroxisomes oxidize medium-, long-, and very-long-chain fatty acids, dicarboxylic fatty acids, branched fatty acids, prostaglandins, xenobiotics, and bile acid intermediates. The chief roles of peroxisomal beta-oxidation are to shorten toxic lipophilic carboxylic acids to facilitate their excretion and to shorten very-long-chain fatty acids prior to mitochondrial beta-oxidation (Mannaerts, G. P. and P. P. van Veldhoven (1993) Biochimie 75:147-158).

[0163] Enzymes involved in beta-oxidation include acyl CoA synthetase, carnitine acyltransferase, acyl CoA dehydrogenases, enoyl CoA hydratases, L-3-hydroxyacyl CoA dehydrogenase, β-ketothiolase, 2,4-dienoyl CoA reductase, and isomerase.

[0164] Lipid Cleavage and Degradation

[0165] Triglycerides are hydrolyzed to fatty acids and glycerol by lipases. Lysophospholipases (LPLs) are widely distributed enzymes that metabolize intracellular lipids, and occur in numerous isoforms. Small isoforms, approximately 15-30 kD, function as hydrolases; large isoforms, those exceeding 60 kD, function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes when it is formed or imported into a cell. LPLs are regulated by lipid factors including acylcarnitine, arachidonic acid, and phosphatidic acid. These lipid factors are signaling molecules important in numerous pathways, including the inflammatory response. (Anderson, R. et al. (1994) Toxicol. Appl. Pharmacol. 125:176-183; Selle, H. et al. (1993); Eur. J. Biochem. 212:411-416.)

[0166] The secretory phospholipase A₂ (PLA2) superfamily comprises a number of heterogeneous enzymes whose common feature is to hydrolyze the sn-2 fatty acid acyl ester bond of phosphoglycerides. Hydrolysis of the glycerophospholipids releases free fatty acids and lysophospholipids. PLA2 activity generates precursors for the biosynthesis of biologically active lipids, hydroxy fatty acids, and platelet-activating factor. PLA2 hydrolysis of the sn-2 ester bond in phospholipids generates free fatty acids, such as arachidonic acid and lysophospholipids.

[0167] Carbon and Carbohydrate Metabolism

[0168] Carbohydrates, including sugars or saccharides, starch, and cellulose, are aldehyde or ketone compounds with multiple hydroxyl groups. The importance of carbohydrate metabolism is demonstrated by the sensitive regulatory system in place for maintenance of blood glucose levels. Two pancreatic hormones, insulin and glucagon, promote increased glucose uptake and storage by cells, and increased glucose release from cells, respectively. Carbohydrates have three important roles in mammalian cells. First, carbohydrates are used as energy stores, fuels, and metabolic intermediates. Carbohydrates are broken down to form energy in glycolysis and are stored as glycogen for later use. Second, the sugars deoxyribose and ribose form part of the structural support of DNA and RNA, respectively. Third, carbohydrate modifications are added to secreted and membrane proteins and lipids as they traverse the secretory pathway. Cell surface carbohydrate-containing macromolecules, including glycoproteins, glycolipids, and transmembrane proteoglycans, mediate adhesion with other cells and with components of the extracellular matrix. The extracellular matrix is comprised of diverse glycoproteins, glycosaminoglycans (GAGs), and carbohydrate-binding proteins which are secreted from the cell and assembled into an organized meshwork in close association with the cell surface. The interaction of the cell with the surrounding matrix profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways controlling cell proliferation and differentiation, tissue construction, and embryonic development.

[0169] Carbohydrate metabolism is altered in several disorders including diabetes mellitus, hyperglycemia, hypoglycemia, galactosemia, galactokinase deficiency, and UDP-galactose-4-epimerase deficiency (Fauci, A. S. et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., pp. 2208-2209). Altered carbohydrate metabolism is associated with cancer. Reduced GAG and proteoglycan expression is associated with human lung carcinomas (Nackaerts, K. et al. (1997) Int. J. Cancer 74:335-345). The carbohydrate determinants sialyl Lewis A and sialyl Lewis X are frequently expressed on human cancer cells (Kannagi, R. (1997) Glycoconj. J. 14:577-584). Alterations of the N-linked carbohydrate core structure of cell surface glycoproteins are linked to colon and pancreatic cancers (Schwarz, R. E. et al. (1996) Cancer Lett. 107:285-291). Reduced expression of the Sda blood group carbohydrate structure in cell surface glycolipids and glycoproteins is observed in gastrointestinal cancer (Dohi, T. et al. (1996) Int. J. Cancer 67:626-663). (Carbon and carbohydrate metabolism is reviewed in Stryer,L. (1995) Biochemistry W. H. Freeman and Company, New York N.Y.; Lehninger, A. L. (1982) Principles of Biochemistry Worth Publishers Inc., New York N.Y.; and Lodish, H. et al. (1995) Molecular Cell Biology Scientific American Books, New York N.Y.)

[0170] Glycolysis

[0171] Enzymes of the glycolytic pathway convert the sugar glucose to pyruvate while simultaneously producing ATP. The pathway also provides building blocks for the synthesis of cellular components such as long-chain fatty acids. After glycolysis, pyrvuate is converted to acetyl-Coenzyme A, which, in aerobic organisms, enters the citric acid cycle. Glycolytic enzymes include hexokinase, phosphoglucose isomerase, phosphofructokinase, aldolase, triose phosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglyceromutase, enolase, and pyruvate kinase. Of these, phosphofructokinase, hexokinase, and pyruvate kinase are important in regulating the rate of glycolysis.

[0172] Gluconeogenesis

[0173] Gluconeogenesis is the synthesis of glucose from noncarbohydrate precursors such as lactate and amino acids. The pathway, which functions mainly in times of starvation and intense exercise, occurs mostly in the liver and kidney. Responsible enzymes include pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose 1,6-bisphosphatase, and glucose-6-phosphatase.

[0174] Pentose Phosphate Pathway

[0175] Pentose phosphate pathway enzymes are responsible for generating the reducing agent NADPH, while at the same time oxidizing glucose-6-phosphate to ribose-5-phosphate. Ribose-5-phosphate and its derivatives become part of important biological molecules such as ATP, Coenzyme A, NAD⁺, FAD, RNA, and DNA. The pentose phosphate pathway has both oxidative and non-oxidative branches. The oxidative branch steps, which are catalyzed by the enzymes glucose-6-phosphate dehydrogenase, lactonase, and 6-phosphogluconate dehydrogenase, convert glucose-6-phosphate and NADP⁺ to ribulose-6-phosphate and NADPH. The non-oxidative branch steps, which are catalyzed by the enzymes phosphopentose isomerase, phosphopentose epimerase, transketolase, and transaldolase, allow the interconversion of three-, four-, five-, six-, and seven-carbon sugars.

[0176] Glucouronate Metabolism

[0177] Glucuronate is a monosaccharide which, in the form of D-glucuronic acid, is found in the GAGs chondroitin and dermatan. D-glucuronic acid is also important in the detoxification and excretion of foreign organic compounds such as phenol. Enzymes involved in glucuronate metabolism include UDP-glucose dehydrogenase and glucuronate reductase.

[0178] Disaccharide Metabolism

[0179] Disaccharides must be hydrolyzed to monosaccharides to be digested. Lactose, a disaccharide found in milk, is hydrolyzed to galactose and glucose by the enzyme lactase. Maltose is derived from plant starch and is hydrolyzed to glucose by the enzyme maltase. Sucrose is derived from plants and is hydrolyzed to glucose and fructose by the enzyme sucrase. Trehalose, a disaccharide found mainly in insects and mushrooms, is hydrolyzed to glucose by the enzyme trehalase (OMIM *275360 Trehalase; Ruf, J. et al. (1990) J. Biol. Chem. 265:15034-15039). Lactase, maltase, sucrase, and trehalase are bound to mucosal cells lining the small intestine, where they participate in the digestion of dietary disaccharides. The enzyme lactose synthetase, composed of the catalytic subunit galactosyltransferase and the modifier subunit α-lactalbumin, converts UDP-galactose and glucose to lactose in the mammary glands.

[0180] Glycogen, Starch, and Chitin Metabolism

[0181] Glycogen is the storage form of carbohydrates in mammals. Mobilization of glycogen maintains glucose levels between meals and during muscular activity. Glycogen is stored mainly in the liver and in skeletal muscle in the form of cytoplasmic granules. These granules contain enzymes that catalyze the synthesis and degradation of glycogen, as well as enzymes that regulate these processes. Enzymes that catalyze the degradation of glycogen include glycogen phosphorylase, a transferase, α-1,6-glucosidase, and phosphoglucomutase. Enzymes that catalyze the synthesis of glycogen include UDP-glucose pyrophosphorylase, glycogen synthetase, a branching enzyme, and nucleoside diphosphokinase. The enzymes of glycogen synthesis and degradation are tightly regulated by the hormones insulin, glucagon, and epinephrine. Starch, a plant-derived polysaccharide, is hydrolyzed to maltose, maltotriose, and α-dextrin by α-amylase, an enzyme secreted by the salivary glands and pancreas. Chitin is a polysaccharide found in insects and crustacea. A chitotriosidase is secreted by macrophages and may play a role in the degradation of chitin-containing pathogens (Boot, R. G. et al. (1995) J. Biol. Chem. 270:26252-26256).

[0182] Peptidoglycans and Glycosaminoglycans

[0183] Glycosaminoglycans (GAGs) are anionic linear unbranched polysaccharides composed of repetitive disaccharide units. These repetitive units contain a derivative of an amino sugar, either glucosamine or galactosamine. GAGs exist free or as part of proteoglycans, large molecules composed of a core protein attached to one or more GAGs. GAGs are found on the cell surface, inside cells, and in the extracellular matrix. Changes in GAG levels are associated with several autoimmune diseases including autoimmune thyroid disease, autoimmune diabetes mellitus, and systemic lupus erythematosus (Hansen, C. et al. (1996) Clin. Exp. Rheum. 14 (Suppl. 15):S59-S67). GAGs include chondroitin sulfate, keratan sulfate, heparin, heparan sulfate, dermatan sulfate, and hyaluronan.

[0184] The GAG hyaluronan (HA) is found in the extracellular matrix of many cells, especially in soft connective tissues, and is abundant in synovial fluid (Pitsillides, A. A. et al. (1993) Int. J. Exp. Pathol. 74:27-34). HA seems to play important roles in cell regulation, development, and differentiation (Laurent, T. C. and J. R. Fraser (1992) FASEB J. 6:2397-2404). Hyaluronidase is an enzyme that degrades HA to oligosaccharides. Hyaluronidases may function in cell adhesion, infection, angiogenesis, signal transduction, reproduction, cancer, and inflammation.

[0185] Proteoglycans, also known as peptidoglycans, are found in the extracellular matrix of connective tissues such as cartilage and are essential for distributing the load in weight-bearing joints. Cell-surface-attached proteoglycans anchor cells to the extracellular matrix. Both extracellular and cell-surface proteoglycans bind growth factors, facilitating their binding to cell-surface receptors and subsequent triggering of signal transduction pathways.

[0186] Amino Acid and Nitrogen Metabolism

[0187] NH₄ ⁺ is assimilated into amino acids by the actions of two enzymes, glutamate dehydrogenase and glutamine synthetase. The carbon skeletons of amino acids come from the intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle. Of the twenty amino acids used in proteins, humans can synthesize only thirteen (nonessential amino acids). The remaining nine must come from the diet (essential amino acids). Enzymes involved in nonessential amino acid biosynthesis include glutamate kinase dehydrogenase, pyrroline carboxylate reductase, asparagine synthetase, phenylalanine oxygenase, methionine adenosyltransferase, adenosylhomocysteinase, cystathionine β-synthase, cystathionine γ-lyase, phosphoglycerate dehydrogenase, phosphoserine transaminase, phosphoserine phosphatase, serine hydroxylmethyltransferase, and glycine synthase.

[0188] Metabolism of amino acids takes place almost entirely in the liver, where the amino group is removed by aminotransferases (transaminases), for example, alanine aminotransferase. The amino group is transferred to α-ketoglutarate to form glutamate. Glutamate dehydrogenase converts glutamate to NH₄ ⁺ and α-ketoglutarate. NH₄ ⁺ is converted to urea by the urea cycle which is catalyzed by the enzymes arginase, ornithine transcarbamoylase, arginosuccinate synthetase, and arginosuccinase. Carbamoyl phosphate synthetase is also involved in urea formation. Enzymes involved in the metabolism of the carbon skeleton of amino acids include serine dehydratase, asparaginase, glutaminase, propionyl CoA carboxylase, methylmalonyl CoA mutase, branched-chain α-keto dehydrogenase complex, isovaleryl CoA dehydrogenase, β-methylcrotonyl CoA carboxylase, phenylalanine hydroxylase, p-hydroxylphenylpyruvate hydroxylase, and homogentisate oxidase.

[0189] Polyamines, which include spermidine, putrescine, and spermine, bind tightly to nucleic acids and are abundant in rapidly proliferating cells. Enzymes involved in polyamine synthesis include ornithine decarboxylase.

[0190] Diseases involved in amino acid and nitrogen metabolism include hyperammonemia, carbamoyl phosphate synthetase deficiency, urea cycle enzyme deficiencies, methylmalonic aciduria, maple syrup disease, alcaptonuria, and phenylketonuria.

[0191] Energy Metabolism

[0192] Cells derive energy from metabolism of ingested compounds that may be roughly categorized as carbohydrates, fats, or proteins. Energy is also stored in polymers such as triglycerides (fats) and glycogen (carbohydrates). Metabolism proceeds along separate reaction pathways connected by key intermediates such as acetyl coenzyme A (acetyl-CoA). Metabolic pathways feature anaerobic and aerobic degradation, coupled with the energy-requiring reactions such as phosphorylation of adenosine diphosphate (ADP) to the triphosphate (ATP) or analogous phosphorylations of guanosine (GDP/GTP), uridine (UDP/UTP), or cytidine (CDP/CTP). Subsequent dephosphorylation of the triphosphate drives reactions needed for cell maintenance, growth, and proliferation.

[0193] Digestive enzymes convert carbohydrates and sugars to glucose; fructose and galactose are converted in the liver to glucose. Enzymes involved in these conversions include galactose-1-phosphate uridyl transferase and UDP-galactose-4 epimerase. In the cytoplasm, glycolysis converts glucose to pyruvate in a series of reactions coupled to ATP synthesis.

[0194] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO₂ with concomitant formation of NADH, FADH₂, and GTP. In oxidative phosphorylation, the transport of electrons from NADH and FADH₂ to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P_(i) by the F₀F₁ ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F₀F₁ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c₁, FeS protein, and cytochrome c oxidase.

[0195] Triglycerides are hydrolyzed to fatty acids and glycerol by lipases. Glycerol is then phosphorylated to glycerol-3-phosphate by glycerol kinase and glycerol phosphate dehydrogenase, and degraded by the glycolysis. Fatty acids are transported into the mitochondria as fatty acyl-carnitine esters and undergo oxidative degradation.

[0196] In addition to metabolic disorders such as diabetes and obesity, disorders of energy metabolism are associated with cancers (Dorward, A. et al. (1997) J. Bioenerg. Biomembr. 29:385-392), autism (Lombard, J. (1998) Med. Hypotheses 50:497-500), neurodegenerative disorders (Alexi, T. et al. (1998) Neuroreport 9:R57-64), and neuromuscular disorders (DiMauro, S. et al. (1998) Biochim. Biophys. Acta 1366:199-210). The myocardium is heavily dependent on oxidative metabolism, so metabolic dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol. 13:190-197).

[0197] For a review of energy metabolism enzymes and intermediates, see Stryer, L. et al. (1995) Biochemistry, W. H. Freeman and Co., San Francisco Calif., pp. 443-652. For a review of energy metabolism regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 744-770.

[0198] Cofactor Metabolism

[0199] Cofactors, including coenzymes and prosthetic groups, are small molecular weight inorganic or organic compounds that are required for the action of an enzyme. Many cofactors contain vitamins as a component. Cofactors include thiamine pyrophosphate, flavin adenine dinucleotide, flavin mononucleotide, nicotinamide adenine dinucleotide, pyridoxal phosphate, coenzyme A, tetrahydrofolate, lipoamide, and heme. The vitamins biotin and cobalamin are associated with enzymes as well. Heme, a prosthetic group found in myoglobin and hemoglobin, consists of protoporphyrin group bound to iron. Porphyrin groups contain four substituted pyrroles covalently joined in a ring, often with a bound metal atom. Enzymes involved in porphyrin synthesis include δ-aminolevulinate synthase, δ-aminolevulinate dehydrase, porphobilinogen deaminase, and cosynthase. Deficiencies in heme formation cause porphyrias. Heme is broken down as a part of erythrocyte turnover. Enzymes involved in heme degradation include heme oxygenase and biliverdin reductase.

[0200] Iron is a required cofactor for many enzymes. Besides the heme-containing enzymes, iron is found in iron-sulfur clusters in proteins including aconitase, succinate dehydrogenase, and NADH-Q reductase. Iron is transported in the blood by the protein transferrin. Binding of transferrin to the transferrin receptor on cell surfaces allows uptake by receptor mediated endocytosis. Cytosolic iron is bound to ferritin protein.

[0201] A molybdenum-containing cofactor (molybdopterin) is found in enzymes including sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. Molybdopterin biosynthesis is performed by two molybdenum cofactor synthesizing enzymes. Deficiencies in these enzymes cause mental retardation and lens dislocation. Other diseases caused by defects in cofactor metabolism include pernicious anemia and methylmalonic aciduria.

[0202] Secretion and Trafficking

[0203] Eukaryotic cells are bound by a lipid bilayer membrane and subdivided into functionally distinct, membrane bound compartments. The membranes maintain the essential differences between the cytosol, the extracellular environment, and the lumenal space of each intracellular organelle. As lipid membranes are highly impermeable to most polar molecules, transport of essential nutrients, metabolic waste products, cell signaling molecules, macromolecules and proteins across lipid membranes and between organelles must be mediated by a variety of transport-associated molecules.

[0204] Protein Trafficking

[0205] In eukaryotes, some proteins are synthesized on ER-bound ribosomes, co-translationally imported into the ER, delivered from the ER to the Golgi complex for post-translational processing and sorting, and transported from the Golgi to specific intracellular and extracellular destinations. All cells possess a constitutive transport process which maintains homeostasis between the cell and its environment. In many differentiated cell types, the basic machinery is modified to carry out specific transport functions. For example, in endocrine glands, hormones and other secreted proteins are packaged into secretory granules for regulated exocytosis to the cell exterior. In macrophage, foreign extracellular material is engulfed (phagocytosis) and delivered to lysosomes for degradation. In fat and muscle cells, glucose transporters are stored in vesicles which fuse with the plasma membrane only in response to insulin stimulation.

[0206] The Secretory Pathway

[0207] Synthesis of most integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on ER-bound ribosomes. These proteins are co-translationally imported into the ER. The proteins leave the ER via membrane-bound vesicles which bud off the ER at specific sites and fuse with each other (homotypic fusion) to form the ER-Golgi Intermediate Compartment (ERGIC). The ERGIC matures progressively through the cis, medial, and trans cisternal stacks of the Golgi, modifying the enzyme composition by retrograde transport of specific Golgi enzymes. In this way, proteins moving through the Golgi undergo post-translational modification, such as glycosylation. The final Golgi compartment is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport vesicles destined for intracellular compartments, such as the lysosome, bud off the TGN. What remains is a secretory vesicle which contains proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurotransmitters, and digestive enzymes. Secretory vesicles eventually fuse with the plasma membrane (Glick, B. S. and V. Malhotra (1998) Cell 95:883-889).

[0208] The secretory process can be constitutive or regulated. Most cells have a constitutive pathway for secretion, whereby vesicles derived from maturation of the TGN require no specific signal to fuse with the plasma membrane. In many cells, such as endocrine cells, digestive cells, and neurons, vesicle pools derived from the TGN collect in the cytoplasm and do not fuse with the plasma membrane until they are directed to by a specific signal.

[0209] Endocytosis

[0210] Endocytosis, wherein cells internalize material from the extracellular environment, is essential for transmission of neuronal, metabolic, and proliferative signals; uptake of many essential nutrients; and defense against invading organisms. Most cells exhibit two forms of endocytosis. The first, phagocytosis, is an actin-driven process exemplified in macrophage and neutrophils. Material to be endocytosed contacts numerous cell surface receptors which stimulate the plasma membrane to extend and surround the particle, enclosing it in a membrane-bound phagosome. In the mammalian immune system, IgG-coated particles bind Fc receptors on the surface of phagocytic leukocytes. Activation of the Fc receptors initiates a signal cascade involving src-family cytosolic kinases and the monomeric GTP-binding (G) protein Rho. The resulting actin reorganization leads to phagocytosis of the particle. This process is an important component of the humoral immune response, allowing the processing and presentation of bacterial-derived peptides to antigen-specific T-lymphocytes.

[0211] The second form of endocytosis, pinocytosis, is a more generalized uptake of material from the external milieu. Like phagocytosis, pinocytosis is activated by ligand binding to cell surface receptors. Activation of individual receptors stimulates an internal response that includes coalescence of the receptor-ligand complexes and formation of clathrin-coated pits. Invagination of the plasma membrane at clathrin-coated pits produces an endocytic vesicle within the cell cytoplasm. These vesicles undergo homotypic fusion to form an early endosomal (EE) compartment. The tubulovesicular EE serves as a sorting site for incoming material. ATP-driven proton pumps in the EE membrane lowers the pH of the EE lumen (pH 6.3-6.8). The acidic environment causes many ligands to dissociate from their receptors. The receptors, along with membrane and other integral membrane proteins, are recycled back to the plasma membrane by budding off the tubular extensions of the EE in recycling vesicles (RV). This selective removal of recycled components produces a carrier vesicle containing ligand and other material from the external environment. The carrier vesicle fuses with TGN-derived vesicles which contain hydrolytic enzymes. The acidic environment of the resulting late endosome (LE) activates the hydrolytic enzymes which degrade the ligands and other material. As digestion takes place, the LE fuses with the lysosome where digestion is completed (Mellman, I. (1996) Annu. Rev. Cell Dev. Biol. 12:575-625).

[0212] Recycling vesicles may return directly to the plasma membrane. Receptors internalized and returned directly to the plasma membrane have a turnover rate of 2-3 minutes. Some RVs undergo microtubule-directed relocation to a perinuclear site, from which they then return to the plasma membrane. Receptors following this route have a turnover rate of 5-10 minutes. Still other RVs are retained within the cell until an appropriate signal is received (Mellman, supra; and James, D. E. et al. (1994) Trends Cell Biol. 4:120-126).

[0213] Vesicle Formation

[0214] Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. The process begins with the budding of a vesicle out of the donor membrane. The membrane-bound vesicle contains proteins to be transported and is surrounded by a protective coat made up of protein subunits recruited from the cytosol. The initial budding and coating processes are controlled by a cytosolic ras-like GTP-binding protein, ADP-ribosylating factor (Arf), and adapter proteins (AP). Different isoforms of both Arf and AP are involved at different sites of budding. Another small G-protein, dynamin, forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to accomplish the final step of the budding process. The coated vesicle complex is then transported through the cytosol. During the transport process, Arf-bound GTP is hydrolyzed to GDP and the coat dissociates from the transport vesicle (West, M. A. et al. (1997) J. Cell Biol. 138:1239-1254). Two different classes of coat protein have also been identified. Clathrin coats form on the TGN and PM surfaces, whereas coatomer or COP coats form on the ER and Golgi. COP coats can further be distinguished as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the ER to the Golgi (Mellman, supra). The COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta′-, gamma-, delta-, epsilon- and zeta-COP. (Harter, C. and F. T. Wieland (1998) Proc. Natl. Acad. Sci. USA 95:11649-11654.)

[0215] Membrane Fusion

[0216] Transport vesicles undergo homotypic or heterotypic fusion in the secretory and endocytotic pathways. Molecules required for appropriate targeting and fusion of vesicles with their target membrane include proteins incorporated in the vesicle membrane, the target membrane, and proteins recruited from the cytosol. During budding of the vesicle from the donor compartment, an integral membrane protein, VAMP (vesicle-associated membrane protein) is incorporated into the vesicle. Soon after the vesicle uncoats, a cytosolic prenylated GTP-binding protein, Rab (a member of the Ras superfamily), is inserted into the vesicle membrane. GTP-bound Rab proteins are directed into nascent transport vesicles where they interact with VAMP. Following vesicle transport, GTPase activating proteins (GAPs) in the target membrane convert Rab proteins to the GDP-bound form. A cytosolic protein, guanine-nucleotide dissociation inhibitor (GDI) helps return GDP-bound Rab proteins to their membrane of origin. Several Rab isoforms have been identified and appear to associate with specific compartments within the cell. Rab proteins appear to play a role in mediating the function of a viral gene, Rev, which is essential for replication of HIV-1, the virus responsible for AIDS (Flavell, R. A. et al. (1996) Proc. Natl. Acad. Sci. USA 93:4421-4424).

[0217] Docking of the transport vesicle with the target membrane involves the formation of a complex between the vesicle SNAP receptor (v-SNARE), target membrane (t-) SNAREs, and certain other membrane and cytosolic proteins. Many of these other proteins have been identified although their exact functions in the docking complex remain uncertain (Tellam, J. T. et al. (1995) J. Biol. Chem. 270:5857-63; and Hata, Y. and T. C. Sudhof (1995) J. Biol. Chem. 270:13022-28). N-ethylmaleimide sensitive factor (NSF) and soluble NSF-attachment protein (α-SNAP and β-SNAP) are two such proteins that are conserved from yeast to man and function in most intracellular membrane fusion reactions. Sec1 represents a family of yeast proteins that function at many different stages in the secretory pathway including membrane fusion. Recently, mammalian homologs of Sec1, called Munc-18 proteins, have been identified (Katagiri, H. et al. (1995) J. Biol. Chem. 270:4963-4966; Hata et al. supra).

[0218] The SNARE complex involves three SNARE molecules, one in the vesicular membrane and two in the target membrane. Synaptotagmin is an integral membrane protein in the synaptic vesicle which associates with the t-SNARE syntaxin in the docking complex. Synaptotagmin binds calcium in a complex with negatively charged phospholipids, which allows the cytosolic SNAP protein to displace synaptotagmin from syntaxin and fusion to occur. Thus, synaptotagmin is a negative regulator of fusion in the neuron (Littleton, J. T. et al. (1993) Cell 74:1125-1134). The most abundant membrane protein of synaptic vesicles appears to be the glycoprotein synaptophysin, a 38 kDa protein with four transmembrane domains.

[0219] Specificity between a vesicle and its target is derived from the v-SNARE, t-SNAREs, and associated proteins involved. Different isoforms of SNAREs and Rabs show distinct cellular and subcellular distributions. VAMP-1/synaptobrevin, membrane-anchored synaptosome-associated protein of 25 kDa (SNAP-25), syntaxin-1, Rab3A, Rabl5, and Rab23 are predominantly expressed in the brain and nervous system. Different syntaxin, VAMP, and Rab proteins are associated with distinct subcellular compartments and their vesicular carriers.

[0220] Nuclear Transport

[0221] Transport of proteins and RNA between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs). NPC-mediated transport occurs in both directions through the nuclear envelope. All nuclear proteins are imported from the cytoplasm, their site of synthesis. tRNA and mRNA are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function. Processing of small nuclear RNAs involves export into the cytoplasm, assembly with proteins and modifications such as hypermethylation to produce small nuclear ribonuclear proteins (snRNPs), and subsequent import of the snRNPs back into the nucleus. The assembly of ribosomes requires the initial import of ribosomal proteins from the cytoplasm, their incorporation with RNA into ribosomal subunits, and export back to the cytoplasm. (Görlich, D. and I. W. Mattaj (1996) Science 271:1513-1518.)

[0222] The transport of proteins and mRNAs across the NPC is selective, dependent on nuclear localization signals, and generally requires association with nuclear transport factors. Nuclear localization signals (NLS) consist of short stretches of amino acids enriched in basic residues. NLS are found on proteins that are targeted to the nucleus, such as the gluc.ocorticoid receptor. The NLS is recognized by the NLS receptor, importin, which then interacts with the monomeric GTP-binding protein Ran. This NLS protein/receptor/Ran complex navigates the nuclear pore with the help of the homodimeric protein nuclear transport factor 2 (NTF2). NTF2 binds the GDP-bound form of Ran and to multiple proteins of the nuclear pore complex containing FXFG repeat motifs, such as p62. (Paschal, B. et al. (1997) J. Biol. Chem. 272:21534-21539; and Wong, D. H. et al. (1997) Mol. Cell Biol. 17:3755-3767). Some proteins are dissociated before nuclear mRNAs are transported across the NPC while others are dissociated shortly after nuclear mRNA transport across the NPC and are reimported into the nucleus.

[0223] Disease Correlation

[0224] The etiology of numerous human diseases and disorders can be attributed to defects in the transport or secretion of proteins. For example, abnormal hormonal secretion is linked to disorders such as diabetes insipidus (vasopressin), hyper- and hypoglycemia (insulin, glucagon), Grave's disease and goiter (thyroid hormone), and Cushing's and Addison's diseases (adrenocorticotropic hormone, ACTH). Moreover, cancer cells secrete excessive amounts of hormones or other biologically active peptides. Disorders related to excessive secretion of biologically active peptides by tumor cells include fasting hypoglycemia due to increased insulin secretion from insulinoma-islet cell tumors; hypertension due to increased epinephrine and norepinephrine secreted from pheochromocytomas of the adrenal medulla and sympathetic paraganglia; and carcinoid syndrome, which is characterized by abdominal cramps, diarrhea, and valvular heart disease caused by excessive amounts of vasoactive substances such as serotonin, bradykinin, histamine, prostaglandins, and polypeptide hormones, secreted from intestinal tumors. Biologically active peptides that are ectopically synthesized in and secreted from tumor cells include ACTH and vasopressin (lung and pancreatic cancers); parathyroid hormone (lung and bladder cancers); calcitonin (lung and breast cancers); and thyroid-stimulating hormone (medullary thyroid carcinoma). Such peptides may be useful as diagnostic markers for tumorigenesis (Schwartz, M. Z. (1997) Semin. Pediatr. Surg. 3:141-146; and Said, S. I. and G. R. Faloona (1975) N. Engl. J. Med. 293:155-160).

[0225] Defective nuclear transport may play a role in cancer. The BRCA1 protein contains three potential NLSs which interact with importin alpha, and is transported into the nucleus by the importin/NPC pathway. In breast cancer cells the BRCA1 protein is aberrantly localized in the cytoplasm. The mislocation of the BRCA1 protein in breast cancer cells may be due to a defect in the NPC nuclear import pathway (Chen, C. F. et al. (1996) J. Biol. Chem. 271:32863-32868).

[0226] It has been suggested that in some breast cancers, the tumor-suppressing activity of p53 is inactivated by the sequestration of the protein in the cytoplasm, away from its site of action in the cell nucleus. Cytoplasmic wild-type p53 was also found in human cervical carcinoma cell lines. (Moll, U. M. et al. (1992) Proc. Natl. Acad. Sci. USA 89:7262-7266; and Liang, X. H. et al. (1993) Oncogene 8:2645-2652.)

[0227] Environmental Responses

[0228] Organisms respond to the environment by a number of pathways. Heat shock proteins, including hsp 70, hsp60, hsp90, and hsp 40, assist organisms in coping with heat damage to cellular proteins.

[0229] Aquaporins (AQP) are channels that transport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes including renal fluid filtration, aqueous humor generation in the eye, cerebrospinal fluid production in the brain, and appropriate hydration of the lung. Aquaporins are members of the major intrinsic protein (MIP) family of membrane transporters (King, L. S. and P. Agre (1996) Annu. Rev. Physiol. 58:619-648; Ishibashi, K. et al. (1997) J. Biol. Chem. 272:20782-20786). The study of aquaporins may have relevance to understanding edema formation and fluid balance in both normal physiology and disease states (King, supra). Mutations in AQP2 cause autosomal recessive nephrogenic diabetes insipidus (OMIM *107777 Aquaporin 2; AQP2). Reduced AQP4 expression in skeletal muscle may be associated with Duchenne muscular dystrophy (Frigeri, A. et al. (1998) J. Clin. Invest. 102:695-703). Mutations in AQP0 cause autosomal dominant cataracts in the mouse (OMIM *154050 Major Intrinsic Protein of Lens Fiber; MIP).

[0230] The metallothioneins (MTs) are a group of small (61 amino acids), cysteine-rich proteins that bind heavy metals such as cadmium, zinc, mercury, lead, and copper and are thought to play a role in metal detoxification or the metabolism and homeostasis of metals. Arsenite-resistance proteins have been identified in hamsters that are resistant to toxic levels of arsenite (Rossman, T. G. et al. (1997) Mutat. Res. 386:307-314).

[0231] Humans respond to light and odors by specific protein pathways. Proteins involved in light perception include rhodopsin, transducin, and cGMP phosphodiesterase. Proteins involved in odor perception include multiple olfactory receptors. Other proteins are important in human Circadian rhythms and responses to wounds.

[0232] Immunity and Host Defense

[0233] All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal and parasitic infections. Included in these systems are the processes of humoral immunity, the complement cascade and the inflammatory response (Paul, W. E. (1993) Fundamental Immunology, Raven Press, Ltd., New York N.Y., pp.1-20).

[0234] The cellular components of the humoral immune system include six different types of leukocytes: monocytes, lymphocytes, polymorphonuclear granulocytes (consisting of neutrophils, eosinophils, and basophils) and plasma cells. Additionally, fragments of megakaryocytes, a seventh type of white blood cell in the bone marrow, occur in large numbers in the blood as platelets.

[0235] Leukocytes are formed from two stem cell lineages in bone marrow. The myeloid stem cell line produces granulocytes and monocytes and, the lymphoid stem cell produces lymphocytes. Lymphoid cells travel to the thymus, spleen and lymph nodes, where they mature and differentiate into lymphocytes. Leukocytes are responsible for defending the body against invading pathogens. Neutrophils and monocytes attack invading bacteria, viruses, and other pathogens and destroy them by phagocytosis. Monocytes enter tissues and differentiate into macrophages which are extremely phagocytic. Lymphocytes and plasma cells are a part of the immune system which recognizes specific foreign molecules and organisms and inactivates them, as well as signals other cells to attack the invaders.

[0236] Granulocytes and monocytes are formed and stored in the bone marrow until needed. Megakaryocytes are produced in bone marrow, where they fragment into platelets and are released into the bloodstream. The main function of platelets is to activate the blood clotting mechanism. Lymphocytes and plasma cells are produced in various lymphogenous organs, including the lymph nodes, spleen, thymus, and tonsils.

[0237] Both neutrophils and macrophages exhibit chemotaxis towards sites of inflammation. Tissue inflammation in response to pathogen invasion results in production of chemo-attractants for leukocytes, such as endotoxins or other bacterial products, prostaglandins, and products of leukocytes or platelets.

[0238] Basophils participate in the release of the chemicals involved in the inflammatory process. The main function of basophils is secretion of these chemicals to such a degree that they have been referred to as “unicellular endocrine glands”. A distinct aspect of basophilic secretion is that the contents of granules go directly into the extracellular environment, not into vacuoles as occurs with neutrophils, eosinophils and monocytes. Basophils have receptors for the Fc fragment of immunoglobulin E (IgE) that are not present on other leukocytes. Crosslinking of membrane IgE with anti-IgE or other ligands triggers degranulation.

[0239] Eosinophils are bi- or multi-nucleated white blood cells which contain eosinophilic granules. Their plasma membrane is characterized by Ig receptors, particularly IgG and IgE. Generally, eosinophils are stored in the bone marrow until recruited for use at a site of inflammation or invasion. They have specific functions in parasitic infections and allergic reactions, and are thought to detoxify some of the substances released by mast cells and basophils which cause inflammation. Additionally, they phagocytize antigen-antibody complexes and further help prevent spread of the inflammation.

[0240] Macrophages are monocytes that have left the blood stream to settle in tissue. Once monocytes have migrated into tissues, they do not re-enter the bloodstream. The mononuclear phagocyte system is comprised of precursor cells in the bone marrow, monocytes in circulation, and macrophages in tissues. The system is capable of very fast and extensive phagocytosis. A macrophage may phagocytize over 100 bacteria, digest them and extrude residues, and then survive for many more months. Macrophages are also capable of ingesting large particles, including red blood cells and malarial parasites. They increase several-fold in size and transform into macrophages that are characteristic of the tissue they have entered, surviving in tissues for several months.

[0241] Mononuclear phagocytes are essential in defending the body against invasion by foreign pathogens, particularly intracellular microorganisms such as M. tuberculosis, listeria, leishmania and toxoplasma. Macrophages can also control the growth of tumorous cells, via both phagocytosis and secretion of hydrolytic enzymes. Another important function of macrophages is that of processing antigen and presenting them in a biochemically modified form to lymphocytes.

[0242] The immune system responds to invading microorganisms in two major ways: antibody production and cell mediated responses. Antibodies are immunoglobulin proteins produced by B-lymphocytes which bind to specific antigens and cause inactivation or promote destruction of the antigen by other cells. Cell-mediated immune responses involve T-lymphocytes (T cells) that react with foreign antigen on the surface of infected host cells. Depending on the type of T cell, the infected cell is either killed or signals are secreted which activate macrophages and other cells to destroy the infected cell (Paul, supra).

[0243] T-lymphocytes originate in the bone marrow or liver in fetuses. Precursor cells migrate via the blood to the thymus, where they are processed to mature into T-lymphocytes. This processing is crucial because of positive and negative selection of T cells that will react with foreign antigen and not with self molecules. After processing, T cells continuously circulate in the blood and secondary lymphoid tissues, such as lymph nodes, spleen, certain epithelium-associated tissues in the gastrointestinal tract, respiratory tract and skin. When T-lymphocytes are presented with the complementary antigen, they are stimulated to proliferate and release large numbers of activated T cells into the lymph system and the blood system. These activated T cells can survive and circulate for several days. At the same time, T memory cells are created, which remain in the lymphoid tissue for months or years. Upon subsequent exposure to that specific antigen, these memory cells will respond more rapidly and with a stronger response than induced by the original antigen. This creates an “immunological memory” that can provide immunity for years.

[0244] There are two major types of T cells: cytotoxic T cells destroy infected host cells, and helper T cells activate other white blood cells via chemical signals. One class of helper cell, T_(H)1, activates macrophages to destroy ingested microorganisms, while another, T_(H)2, stimulates the production of antibodies by B cells.

[0245] Cytotoxic T cells directly attack the infected target cell. In virus-infected cells, peptides derived from viral proteins are generated by the proteasome. These peptides are transported into the ER by the transporter associated with antigen processing (TAP) (Pamer, E. and P. Cresswell (1998) Annu. Rev. Immunol. 16:323-358). Once inside the ER, the peptides bind MHC I chains, and the peptide/MHC I complex is transported to the cell surface. Receptors on the surface of T cells bind to antigen presented on cell surface MHC molecules. Once activated by binding to antigen, T cells secrete γ-interferon, a signal molecule that induces the expression of genes necessary for presenting viral (or other) antigens to cytotoxic T cells. Cytotoxic T cells kill the infected cell by stimulating programmed cell death.

[0246] Helper T cells constitute up to 75% of the total T cell population. They regulate the immune functions by producing a variety of lymphokines that act on other cells in the immune system and on bone marrow. Among these lymphokines are: interleukins-2,3,4,5,6; granulocyte-monocyte colony stimulating factor, and γ-interferon.

[0247] Helper T cells are required for most B cells to respond to antigen. When an activated helper cell contacts a B cell, its centrosome and Golgi apparatus become oriented toward the B cell, aiding the directing of signal molecules, such as transmembrane-bound protein called CD40 ligand, onto the B cell surface to interact with the CD40 transmembrane protein. Secreted signals also help B cells to proliferate and mature and, in some cases, to switch the class of antibody being produced.

[0248] B-lymphocytes (B cells) produce antibodies which react with specific antigenic proteins presented by pathogens. Once activated, B cells become filled with extensive rough endoplasmic reticulum and are known as plasma cells. As with T cells, interaction of B cells with antigen stimulates proliferation of only those B cells which produce antibody specific to that antigen. There are five classes of antibodies, known as immunoglobulins, which together comprise about 20% of total plasma protein. Each class mediates a characteristic biological response after antigen binding. Upon activation by specific antigen B cells switch from making membrane-bound antibody to secretion of that antibody.

[0249] Antibodies, or immunoglobulins (Ig), are the founding members of the Ig superfamily and the central components of the humoral immune response. Antibodies are either expressed on the surface of B cells or secreted by B cells into the circulation. Antibodies bind and neutralize blood-borne foreign antigens. The prototypical antibody is a tetramer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds.

[0250] This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, IgE, IgG and IgM, are defined by the α, δ, ε, γ, and μ H-chain types. There are two types of L-chains, κ and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tetrameric, while the other classes of antibodies are generally variants or multimers of this basic structure.

[0251] H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant region. Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region. In addition, H chains such as μ have been shown to associate with other polypeptides during differentiation of the B cell.

[0252] Antibodies can be described in terms of their two main functional domains. Antigen recognition is mediated by the Fab (antigen binding fragment) region of the antibody, while effector functions are mediated by the Fc (crystallizable fragment) region. Binding of antibody to an antigen, such as a bacterium, triggers the destruction of the antigen by phagocytic white blood cells such as macrophages and neutrophils. These cells express surface receptors that specifically bind to the antibody Fc region and allow the phagocytic cells to engulf, ingest, and degrade the antibody-bound antigen. The Fe receptors expressed by phagocytic cells are single-pass transmembrane glycoproteins of about 300 to 400 amino acids (Sears, D. W. et al. (1990) J. Immunol. 144:371-378). The extracellular portion of the Fe receptor typically contains two or three Ig domains.

[0253] Diseases which cause over- or under-abundance of any one type of leukocyte usually result in the entire immune defense system becoming involved. A well-known autoimmune disease is AIDS (Acquired Immunodeficiency Syndrome) where the number of helper T cells is depleted, leaving the patient susceptible to infection by microorganisms and parasites. Another widespread medical condition attributable to the immune system is that of allergic reactions to certain antigens. Allergic reactions include: hay fever, asthma, anaphylaxis, and urticaria (hives). Leukemias are an excess production of white blood cells, to the point where a major portion of the body's metabolic resources are directed solely at proliferation of white blood cells, leaving other tissues to starve. Leukopenia or agranulocytosis occurs when the bone marrow stops producing white blood cells. This leaves the body unprotected against foreign microorganisms, including those which normally inhabit skin, mucous membranes, and gastrointestinal tract. If all white blood cell production stops completely, infection will occur within two days and death may follow only 1 to 4 days later.

[0254] Impaired phagocytosis occurs in several diseases, including monocytic leukemia, systemic lupus, and granulomatous disease. In such a situation, macrophages can phagocytize normally, but the enveloped organism is not killed. A defect in the plasma membrane enzyme which converts oxygen to lethally reactive forms results in abscess formation in liver, lungs, spleen, lymph nodes, and beneath the skin. Eosinophilia is an excess of eosinophils commonly observed in patients with allergies (hay fever, asthma), allergic reactions to drugs, rheumatoid arthritis, and cancers (Hodgkin's disease, lung, and liver cancer) (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York N.Y.).

[0255] Host defense is further augmented by the complement system. The complement system serves as an effector system and is involved in infectious agent recognition. It can function as an independent immune network or in conjunction with other humoral immune responses. The complement system is comprised of numerous plasma and membrane proteins that act in a cascade of reaction sequences whereby one component activates the next. The result is a rapid and amplified response to infection through either an inflammatory response or increased phagocytosis.

[0256] The complement system has more than 30 protein components which can be divided into functional groupings including modified serine proteases, membrane-binding proteins and regulators of complement activation. Activation occurs through two different pathways the classical and the alternative. Both pathways serve to destroy infectious agents through distinct triggering mechanisms that eventually merge with the involvement of the component C3.

[0257] The classical pathway requires antibody binding to infectious agent antigens. The antibodies serve to define the target and initiate the complement system cascade, culminating in the destruction of the infectious agent. In this pathway, since the antibody guides initiation of the process, the complement can be seen as an effector arm of the humoral immune system.

[0258] The alternative pathway of the complement system does not require the presence of pre-existing antibodies for targeting infectious agent destruction. Rather, this pathway, through low levels of an activated component, remains constantly primed and provides surveillance in the non-immune host to enable targeting and destruction of infectious agents. In this case foreign material triggers the cascade, thereby facilitating phagocytosis or lysis (Paul, supra, pp.918-919).

[0259] Another important component of host defense is the process of inflammation. Inflammatory responses are divided into four categories on the basis of pathology and include allergic inflammation, cytotoxic antibody mediated inflammation, immune complex mediated inflammation and monocyte mediated inflammation. Inflammation manifests as a combination of each of these forms with one predominating.

[0260] Allergic acute inflammation is observed in individuals wherein specific antigens stimulate IgE antibody production. Mast cells and basophils are subsequently activated by the attachment of antigen-IgE complexes, resulting in the release of cytoplasmic granule contents such as histamine. The products of activated mast cells can increase vascular permeability and constrict the smooth muscle of breathing passages, resulting in anaphylaxis or asthma. Acute inflammation is also mediated by cytotoxic antibodies and can result in the destruction of tissue through the binding of complement-fixing antibodies to cells. The responsible antibodies are of the IgG or IgM types. Resultant clinical disorders include autoimmune hemolytic anemia and thrombocytopenia as associated with systemic lupus erythematosis.

[0261] Immune complex mediated acute inflammation involves the IgG or IgM antibody types which combine with antigen to activate the complement cascade. When such immune complexes bind to neutrophils and macrophages they activate the respiratory burst to form protein- and vessel-damaging agents such as hydrogen peroxide, hydroxyl radical, hypochlorous acid, and chloramines. Clinical manifestations include rheumatoid arthritis and systemic lupus erythematosus.

[0262] In chronic inflammation or delayed-type hypersensitivity, macrophages are activated and process antigen for presentation to T cells that subsequently produce lymphokines and monokines. This type of inflammatory response is likely important for defense against intracellular parasites and certain viruses. Clinical associations include, granulomatous disease, tuberculosis, leprosy, and sarcoidosis (Paul, W. E., supra, pp.1017-1018).

[0263] Extracellular Information Transmission Molecules

[0264] Intercellular communication is essential for the growth and survival of multicellular organisms, and in particular, for the function of the endocrine, nervous, and immune systems. In addition, intercellular communication is critical for developmental processes such as tissue construction and organogenesis, in which cell proliferation, cell differentiation, and morphogenesis must be spatially and temporally regulated in a precise and coordinated manner. Cells communicate with one another through the secretion and uptake of diverse types of signaling molecules such as hormones, growth factors, neuropeptides, and cytokines.

[0265] Hormones

[0266] Hormones are signaling molecules that coordinately regulate basic physiological processes from embryogenesis throughout adulthood. These processes include metabolism, respiration, reproduction, excretion, fetal tissue differentiation and organogenesis, growth and development, homeostasis, and the stress response. Hormonal secretions and the nervous system are tightly integrated and interdependent. Hormones are secreted by endocrine glands, primarily the hypothalamus and pituitary, the thyroid and parathyroid, the pancreas, the adrenal glands, and the ovaries and testes.

[0267] The secretion of hormones into the circulation is tightly controlled. Hormones are often secreted in diurnal, pulsatile, and cyclic patterns. Hormone secretion is regulated by perturbations in blood biochemistry, by other upstream-acting hormones, by neural impulses, and by negative feedback loops. Blood hormone concentrations are constantly monitored and adjusted to maintain optimal, steady-state levels. Once secreted, hormones act only on those target cells that express specific receptors.

[0268] Most disorders of the endocrine system are caused by either hyposecretion or hypersecretion of hormones. Hyposecretion often occurs when a hormone's gland of origin is damaged or otherwise impaired. Hypersecretion often results from the proliferation of tumors derived from hormone-secreting cells. Inappropriate hormone levels may also be caused by defects in regulatory feedback loops or in the processing of hormone precursors. Endocrine malfunction may also occur when the target cell fails to respond to the hormone.

[0269] Hormones can be classified biochemically as polypeptides, steroids, eicosanoids, or amines. Polypeptides, which include diverse hormones such as insulin and growth hormone, vary in size and function and are often synthesized as inactive precursors that are processed intracellularly into mature, active forms. Amines, which include epinephrine and dopamine, are amino acid derivatives that function in neuroendocrine signaling. Steroids, which include the cholesterol-derived hormones estrogen and testosterone, function in sexual development and reproduction. Eicosanoids, which include prostaglandins and prostacyclins, are fatty acid derivatives that function in a variety of processes. Most polypeptides and some amines are soluble in the circulation where they are highly susceptible to proteolytic degradation within seconds after their secretion. Steroids and lipids are insoluble and must be transported in the circulation by carrier proteins. The following discussion will focus primarily on polypeptide hormones.

[0270] Hormones secreted by the hypothalamus and pituitary gland play a critical role in endocrine function by coordinately regulating hormonal secretions from other endocrine glands in response to neural signals. Hypothalamic hormones include thyrotropin-releasing hormone, gonadotropin-releasing hormone, somatostatin, growth-hormone releasing factor, corticotropin-releasing hormone, substance P, dopamine, and prolactin-releasing hormone. These hormones directly regulate the secretion of hormones from the anterior lobe of the pituitary. Hormones secreted by the anterior pituitary include adrenocorticotropic hormone (ACTH), melanocyte-stimulating hormone, somatotropic hormones such as growth hormone and prolactin, glycoprotein:hormones such as thyroid-stimulating hormone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH), β-lipotropin, and β-endorphins. These hormones regulate hormonal secretions from the thyroid, pancreas, and adrenal glands, and act directly on the reproductive organs to stimulate ovulation and spermatogenesis. The posterior pituitary synthesizes and secretes antidiuretic hormone (ADH, vasopressin) and oxytocin.

[0271] Disorders of the hypothalamus and pituitary often result from lesions such as primary brain tumors, adenomas, infarction associated with pregnancy, hypophysectomy, aneurysms, vascular malformations, thrombosis, infections, immunological disorders, and complications due to head trauma. Such disorders have profound effects on the function of other endocrine glands. Disorders associated with hypopituitarism include hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism. Disorders associated with hyperpituitarism include acromegaly, giantism, and syndrome of inappropriate ADH secretion (SIADH), often caused by benign adenomas.

[0272] Hormones secreted by the thyroid and parathyroid primarily control metabolic rates and the regulation of serum calcium levels, respectively. Thyroid hormones include calcitonin, somatostatin, and thyroid hormone. The parathyroid secretes parathyroid hormone. Disorders associated with hypothyroidism include goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism. Disorders associated with hyperthyroidism include thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease. Disorders associated with hyperparathyroidism include Conn disease (chronic hypercalemia) leading to bone resorption and parathyroid hyperplasia.

[0273] Hormones secreted by the pancreas regulate blood glucose levels by modulating the rates of carbohydrate, fat, and protein metabolism. Pancreatic hormones include insulin, glucagon, amylin, γ-aminobutyric acid, gastrin, somatostatin, and pancreatic polypeptide. The principal disorder associated with pancreatic dysfunction is diabetes mellitus caused by insufficient insulin activity. Diabetes mellitus is generally classified as either Type I (insulin-dependent, juvenile diabetes) or Type II (non-insulin-dependent, adult diabetes). The treatment of both forms by insulin replacement therapy is well known. Diabetes mellitus often leads to acute complications such as hypoglycemia (insulin shock), coma, diabetic ketoacidosis, lactic acidosis, and chronic complications leading to disorders of the eye, kidney, skin, bone, joint, cardiovascular system, nervous system, and to decreased resistance to infection.

[0274] The anatomy, physiology, and diseases related to hormonal function are reviewed in McCance, K. L. and S. E. Huether (1994) Pathophysiology: The Biological Basis for Disease in Adults and Children, Mosby-Year Book, Inc., St. Louis Mo.; Greenspan, F. S. and J. D. Baxter (1994) Basic and Clinical Endocrinology, Appleton and Lange, East Norwalk Conn.

[0275] Growth Factors

[0276] Growth factors are secreted proteins that mediate intercellular communication. Unlike hormones, which travel great distances via the circulatory system, most growth factors are primarily local mediators that act on neighboring cells. Most growth factors contain a hydrophobic N-terminal signal peptide sequence which directs the growth factor into the secretory pathway. Most growth factors also undergo post-translational modifications within the secretory pathway. These modifications can include proteolysis, glycosylation, phosphorylation, and intramolecular disulfide bond formation. Once secreted, growth factors bind to specific receptors on the surfaces of neighboring target cells, and the bound receptors trigger intracellular signal transduction pathways. These signal transduction pathways elicit specific cellular responses in the target cells. These responses can include the modulation of gene expression and the stimulation or inhibition of cell division, cell differentiation, and cell motility.

[0277] Growth factors fall into at least two broad and overlapping classes. The broadest class includes the large polypeptide growth factors, which are wide-ranging in their effects. These factors include epidermal growth factor (EGF), fibroblast growth factor (FGF), transforming growth factor-β (TGF-β), insulin-like growth factor (IGF), nerve growth factor (NGF), and platelet-derived growth factor (PDGF), each defining a family of numerous related factors. The large polypeptide growth factors, with the exception of NGF, act as mitogens on diverse cell types to stimulate wound healing, bone synthesis and remodeling, extracellular matrix synthesis, and proliferation of epithelial, epidermal, and connective tissues. Members of the TGF-β, EGF, and FGF families also function as inductive signals in the differentiation of embryonic tissue. NGF functions specifically as a neurotrophic factor, promoting neuronal growth and differentiation.

[0278] Another class of growth factors includes the hematopoietic growth factors, which are narrow in their target specificity. These factors stimulate the proliferation and differentiation of blood cells such as B-lymphocytes, T-lymphocytes, erythrocytes, platelets, eosinophils, basophils, neutrophils, macrophages, and their stem cell precursors. These factors include the colony-stimulating factors (G-CSF, M-CSF, GM-CSF, and CSF1-3), erythropoietin, and the cytokines. The cytokines are specialized hematopoietic factors secreted by cells of the immune system and are discussed in detail below.

[0279] Growth factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo. Overexpression of the large polypeptide growth factors promotes the proliferation and transformation of cells in culture. Inappropriate expression of these growth factors by tumor cells in vivo may contribute to tumor vascularization and metastasis. Inappropriate activity of hematopoietic growth factors can result in anemias, leukemias, and lymphomas. Moreover, growth factors are both structurally and functionally related to oncoproteins, the potentially cancer-causing products of proto-oncogenes. Certain FGF and PDGF family members are themselves homologous to oncoproteins, whereas receptors for some members of the EGF, NGF, and FGF families are encoded by proto-oncogenes. Growth factors also affect the transcriptional regulation of both proto-oncogenes and oncosuppressor genes (Pimentel, E. (1994) Handbook of Growth Factors, CRC Press, Ann Arbor Mich.; McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford University Press, New York N.Y.; Habenicht, A., ed. (1990) Growth Factors, Differentiation Factors, and Cytokines, Springer-Verlag, New York N.Y.).

[0280] In addition, some of the large polypeptide growth factors play crucial roles in the induction of the primordial germ layers in the developing embryo. This induction ultimately results in the formation of the embryonic mesoderm, ectoderm, and endoderm which in turn provide the framework for the entire adult body plan. Disruption of this inductive process would be catastrophic to embryonic development.

[0281] Small Peptide Factors-Neuropeptides and Vasomediators

[0282] Neuropeptides and vasomediators (NP/VM) comprise a family of small peptide factors, typically of 20 amino acids or less. These factors generally function in neuronal excitation and inhibition of vasoconstriction/vasodilation, muscle contraction, and hormonal secretions from the brain and other endocrine tissues. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endothelins, formyl-methionyl peptides, glucagon, cholecystokinin, gastrin, and many of the peptide hormones discussed above. NP/VMs can transduce signals directly, modulate the activity or release of other neurotransmitters and hormones, and act as catalytic enzymes in signaling cascades. The effects of NP/VMs range from extremely brief to long-lasting. (Reviewed in Martin, C. R. et al. (1985) Endocrine Physiology, Oxford University Press, New York N.Y., pp. 57-62.)

[0283] Cytokines

[0284] Cytokines comprise a family of signaling molecules that modulate the immune system and the inflammatory response. Cytokines are usually secreted by leukocytes, or white blood cells, in response to injury or infection. Cytokines function as growth and differentiation factors that act primarily on cells of the immune system such as B- and T-lymphocytes, monocytes, macrophages, and granulocytes. Like other signaling molecules, cytokines bind to specific plasma membrane receptors and trigger intracellular signal transduction pathways which alter gene expression patterns. There is considerable potential for the use of cytokines in the treatment of inflammation and immune system disorders.

[0285] Cytokine structure and function have been extensively characterized in vitro. Most cytokines are small polypeptides of about 30 kilodaltons or less. Over 50 cytokines have been identified from human and rodent sources. Examples of cytokine subfamilies include the interferons (IFN-α, -β, and - γ), the interleukins (IL1-IL13), the tumor necrosis factors. (TNF-α and -β), and the chemokines. Many cytokines have been produced using recombinant DNA techniques, and the activities of individual cytokines have been determined in vitro. These activities include regulation of leukocyte proliferation, differentiation, and motility.

[0286] The activity of an individual cytokine in vitro may not reflect the full scope of that cytokine's activity in vivo. Cytokines are not expressed individually in vivo but are instead expressed in combination with a multitude of other cytokines when the organism is challenged with a stimulus. Together, these cytokines collectively modulate the immune response in a manner appropriate for that particular stimulus. Therefore, the physiological activity of a cytokine is determined by the stimulus itself and by complex interactive networks among co-expressed cytokines which may demonstrate both synergistic and antagonistic relationships.

[0287] Chemokines comprise a cytokine subfamily with over 30 members. (Reviewed in Wells, T. N. C. and M. C. Peitsch (1997) J. Leukoc. Biol. 61:545-550.) Chemokines were initially identified as chemotactic proteins that recruit monocytes and macrophages to sites of inflammation. Recent evidence indicates that chemokines may also play key roles in hematopoiesis and HIV-1 infection. Chemokines are small proteins which range from about 6-15 kilodaltons in molecular weight. Chemokines are further classified as C, CC, CXC, or CX₃C based on the number and position of critical cysteine residues. The CC chemokines, for example, each contain a conserved motif consisting of two consecutive cysteines followed by two additional cysteines which occur downstream at 24- and 16-residue intervals, respectively (ExPASy PROSITE database, documents PS00472 and PDOC00434). The presence and spacing of these four cysteine residues are highly conserved, whereas the intervening residues diverge significantly. However, a conserved tyrosine located about 15 residues downstream of the cysteine doublet seems to be important for chemotactic activity. Most of the human genes encoding CC chemokines are clustered on chromosome 17, although there are a few examples of CC chemokine genes that map elsewhere. Other chemokines include lymphotactin (C chemokine); macrophage chemotactic and activating factor (MCAF/MCP-1; CC chemokine); platelet factor 4 and IL-8 (CXC chemokines); and fractalkine and neurotractin (CX₃C chemokines). (Reviewed in Luster, A. D. (1998) N. Engl. J. Med. 338:436-445.)

[0288] Receptor Molecules

[0289] SEQ ID NO:6 and SEQ ID NO:7 encode, for example, receptor molecules.

[0290] The term receptor describes proteins that specifically recognize other molecules. The category is broad and includes proteins with a variety of functions. The bulk of receptors are cell surface proteins which bind extracellular ligands and produce cellular responses in the areas of growth, differentiation, endocytosis, and immune response. Other receptors facilitate the selective transport of proteins out of the endoplasmic reticulum and localize enzymes to particular locations in the cell. The term may also be applied to proteins which act as receptors for ligands with known or unknown chemical composition and which interact with other cellular components. For example, the steroid hormone receptors bind to and regulate transcription of DNA.

[0291] Regulation of cell proliferation, differentiation, and migration is important for the formation and function of tissues. Regulatory proteins such as growth factors coordinately control these cellular processes and act as mediators in cell-cell signaling pathways. Growth factors are secreted proteins that bind to specific cell-surface receptors on target cells. The bound receptors trigger intracellular signal transduction pathways which activate various downstream effectors that regulate gene expression, cell division, cell differentiation, cell motility, and other cellular processes.

[0292] Cell surface receptors are typically integral plasma membrane proteins. These receptors recognize hormones such as catecholamines; peptide hormones; growth and differentiation factors; small peptide factors such as thyrotropin-releasing hormone; galanin, somatostatin, and tachykinins; and circulatory system-borne signaling molecules. Cell surface receptors on immune system cells recognize antigens, antibodies, and major histocompatibility complex (MHC)-bound peptides. Other cell surface receptors bind ligands to be internalized by the cell. This receptor-mediated endocytosis functions in the uptake of low density lipoproteins (LDL), transferrin, glucose- or mannose-terninal glycoproteins, galactose-terminal glycoproteins, immunoglobulins, phosphovitellogenins, fibrin, proteinase-inhibitor complexes, plasminogen activators, and thrombospondin (Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., p. 723; Mikhailenko, I. et al. (1997) J. Biol. Chem. 272:6784-6791).

[0293] Receptor Protein Kinases

[0294] Many growth factor receptors, including receptors for epidermal growth factor, platelet-derived growth factor, fibroblast growth factor, as well as the growth modulator α-thrombin, contain intrinsic protein kinase activities. When growth factor binds to the receptor, it triggers the autophosphorylation of a serine, threonine, or tyrosine residue on the receptor. These phosphorylated sites are recognition sites for the binding of other cytoplasmic signaling proteins. These proteins participate in signaling pathways that eventually link the initial receptor activation at the cell surface to the activation of a specific intracellular target molecule. In the case of tyrosine residue autophosphorylation, these signaling proteins contain a common domain referred to as a Src homology (SH) domain. SH2 domains and SH3 domains are found in phospholipase C-γ, PI-3-K p85 regulatory subunit, Ras-GTPase activating protein, and pp60^(c-src) (Lowenstein, E. J. et al. (1992) Cell 70:431-442). The cytokine family of receptors share a different common binding domain and include transmembrane receptors for growth hormone (GH), interleukins, erythropoietin, and prolactin.

[0295] Other receptors and second messenger-binding proteins have intrinsic serine/threonine protein kinase activity. These include activin/TGF-β/BMP-superfamily receptors, calcium- and diacylglycerol-activated/phospholipid-dependant protein kinase (PK-C), and RNA-dependant protein kinase (PK-R). In addition, other serine/threonine protein kinases, including nematode Twitchin, have fibronectin-like, immunoglobulin C2-like domains.

[0296] G-Protein Coupled Receptors

[0297] G-protein coupled receptors (GPCRs) are integral membrane proteins characterized by the presence of seven hydrophobic transmembrane domains which span the plasma membrane and form a bundle of antiparallel alpha (α) helices. These proteins range in size from under 400 to over 1000 amino acids (Strosberg, A. D. (1991) Eur. J. Biochem. 196:1-10; Coughlin, S. R. (1994) Curr. Opin. Cell Biol. 6:191-197). The amino-terminus of the GPCR is extracellular, of variable length and often glycosylated; the carboxy-terminus is cytoplasmic and generally phosphorylated. Extracellular loops of the GPCR alternate with intracellular loops and link the transmembrane domains. The most conserved domains of GPCRs are the transmembrane domains and the first two cytoplasmic loops. The transmembrane domains account for structural and functional features of the receptor. In most cases, the bundle of a helices forms a binding pocket. In addition, the extracellular N-terminal segment or one or more of the three extracellular loops may also participate in ligand binding. Ligand binding activates the receptor by inducing a conformational change in intracellular portions of the receptor. The activated receptor, in turn, interacts with an intracellular heterotrimeric guanine nucleotide binding (G) protein complex which mediates further intracellular signaling activities, generally the production of second messengers such as cyclic AMP (cAMP), phospholipase C, inositol triphosphate, or interactions with ion channel proteins (Baldwin, J. M. (1994) Curr. Opin. Cell Biol. 6:180-190).

[0298] GPCRs include those for acetylcholine, adenosine, epinephrine and norepinephrine, bombesin, bradykinin, chemokines, dopamine, endothelin, y-aminobutyric acid (GABA), follicle-stimulating hormone (FSH), glutamate, gonadotropin-releasing hormone (GnRH), hepatocyte growth factor, histamine, leukotrienes, melanocortins, neuropeptide Y, opioid peptides, opsins, prostanoids, serotonin, somatostatin, tachykinins, thrombin, thyrotropin-releasing hormone (TRH), vasoactive intestinal polypeptide family, vasopressin and oxytocin, and orphan receptors.

[0299] GPCR mutations, which may cause loss of function or constitutive activation, have been associated with numerous human diseases (Coughlin, supra). For instance, retinitis pigmentosa may arise from mutations in the rhodopsin gene. Rhodopsin is the retinal photoreceptor which is located within the discs of the eye rod cell. Parma, J. et al. (1993, Nature 365:649-651) report that somatic activating mutations in the thyrotropin receptor cause hyperfunctioning thyroid adenomas and suggest that certain GPCRs susceptible to constitutive activation may behave as protooncogenes.

[0300] Nuclear Receptors

[0301] Nuclear receptors bind small molecules such as hormones or second messengers, leading to increased receptor-binding affinity to specific chromosomal DNA elements. In addition the affinity for other nuclear proteins may also be altered. Such binding and protein-protein interactions may regulate and modulate gene expression. Examples of such receptors include the steroid hormone receptors family, the retinoic acid receptors family, and the thyroid hormone receptors family.

[0302] Ligand-Gated Receptor Ion Channels

[0303] Ligand-gated receptor ion channels fall into two categories. The first category, extracellular ligand-gated receptor ion channels (ELGs), rapidly transduce neurotransmitter-binding events into electrical signals, such as fast synaptic neurotransmission. ELG function is regulated by post-translational modification. The second category, intracellular ligand-gated receptor ion channels (ILGs), are activated by many intracellular second messengers and do not require post-translational modification(s) to effect a channel-opening response.

[0304] ELGs depolarize excitable cells to the threshold of action potential generation. In non-excitable cells, ELGs permit a limited calcium ion-influx during the presence of agonist. ELGs include channels directly gated by neurotransmitters such as acetylcholine, L-glutamate, glycine, ATP, serotonin, GABA, and histamine. ELG genes encode proteins having strong structural and functional similarities. ILGs are encoded by distinct and unrelated gene families and include receptors for cAMP, cGMP, calcium ions, ATP, and metabolites of arachidonic acid.

[0305] Macrophage Scavenger Receptors

[0306] Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain. The extracellular domain contains a short spacer domain, an α-helical coiled-coil domain, and a triple helical collagenous domain. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phospholipids, and asbestos (Matsumoto, A. et al. (1990) Proc. Natl. Acad. Sci. USA 87:9133-9137; Elomaa, O. et al. (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa.

[0307] T-Cell Receptors

[0308] T cells play a dual role in the immune system as effectors and regulators, coupling antigen recognition with the transmission of signals that induce cell death in infected cells and stimulate proliferation of other immune cells. Although a population of T cells can recognize a wide range of different antigens, an individual T cell can only recognize a single antigen and only when it is presented to the T cell receptor (TCR) as a peptide complexed with a major histocompatibility molecule (MHC) on the surface of an antigen presenting cell. The TCR on most T cells consists of immunoglobulin-like integral membrane glycoproteins containing two polypeptide subunits, α and β, of similar molecular weight. Both TCR subunits have an extracellular domain containing both variable and constant regions, a transmembrane domain that traverses the membrane once, and a short intracellular domain (Saito, H. et al. (1984) Nature 309:757-762). The genes for the TCR subunits are constructed through somatic rearrangement of different gene segments. Interaction of antigen in the proper MHC context with the TCR initiates signaling cascades that induce the proliferation, maturation, and function of cellular components of the immune system (Weiss, A. (1991) Annu. Rev. Genet. 25:487-510). Rearrangements in TCR genes and alterations in TCR expression have been noted in lymphomas, leukemias, autoimmune disorders, and immunodeficiency disorders (Aisenberg, A. C. et al. (1985) N. Engl. J. Med. 313:529-533; Weiss, supra).

[0309] Intracellular Signaling Molecules

[0310] SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12 encode, for example, intracellular signaling molecules.

[0311] Intracellular signaling is the general process by which cells respond to extracellular signals (hormones, neurotransmitters, growth and differentiation factors, etc.) through a cascade of biochemical reactions that begins with the binding of a signaling molecule to a cell membrane receptor and ends with the activation of an intracellular target molecule. Intermediate steps in the process involve the activation of various cytoplasmic proteins by phosphorylation via protein kinases, and their deactivation by protein phosphatases, and the eventual translocation of some of these activated proteins to the cell nucleus where the transcription of specific genes is triggered. The intracellular signaling process regulates all types of cell functions including cell proliferation, cell differentiation, and gene transcription, and involves a diversity of molecules including protein kinases and phosphatases, and second messenger molecules, such as cyclic nucleotides, calcium-calmodulin, inositol, and various mitogens, that regulate protein phosphorylation.

[0312] Protein Phosphorylation

[0313] Protein kinases and phosphatases play a key role in the intracellular signaling process by controlling the phosphorylation and activation of various signaling proteins. The high energy phosphate for this reaction is generally transferred from the adenosine triphosphate molecule (ATP) to a particular protein by a protein kinase and removed from that protein by a protein phosphatase. Protein. kinases are roughly divided into two groups: those that phosphorylate tyrosine residues (protein tyrosine kinases, PTK) and those that phosphorylate serine or threonine residues (serine/threonine kinases, STK). A few protein kinases have dual specificity for serine/threonine and tyrosine residues. Almost all kinases contain a conserved 250-300 amino acid catalytic domain containing specific residues and sequence motifs characteristic of the kinase family (Hardie, G. and S. Hanks (1995) The Protein Kinase Facts Books, Vol 1:7-20, Academic Press, San Diego Calif.).

[0314] STKs include the second messenger dependent protein kinases such as the cyclic-AMP dependent protein kinases (PKA), involved in mediating hormone-induced cellular responses; calcium-calmodulin (CaM) dependent protein kinases, involved in regulation of smooth muscle contraction, glycogen breakdown, and neurotransmission; and the mitogen-activated protein kinases (MAP) which mediate signal transduction from the cell surface to the nucleus via phosphorylation cascades. Altered PKA expression is implicated in a variety of disorders and diseases including cancer, thyroid disorders, diabetes, atherosclerosis, and cardiovascular disease (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., pp. 416-431, 1887).

[0315] PTKs are divided into transmembrane, receptor PTKs and nontransmembrane, non-receptor PTKs. Transmembrane PTKs are receptors for most growth factors. Non-receptor PTKs lack transmembrane regions and, instead, form complexes with the intracellular regions of cell surface receptors. Receptors that function through non-receptor PTKs include those for cytokines and hormones (growth hormone and prolactin) and antigen-specific receptors on T and B lymphocytes. Many of these PTKs were first identified as the products of mutant oncogenes in cancer cells in which their activation was no longer subject to normal cellular controls. In fact, about one third of the known oncogenes encode PTKs, and it is well known that cellular transformation (oncogenesis) is often accompanied by increased tyrosine phosphorylation activity (Charbonneau, H. and N. K. Tonks (1992) Annu. Rev. Cell Biol. 8:463-493).

[0316] An additional family of protein kinases previously thought to exist only in procaryotes is the histidine protein kinase family (HPK). HPKs bear little homology with mammalian STKs or PTKs but have distinctive sequence motifs of their own (Davie, J. R. et al. (1995) J. Biol. Chem. 270:19861-19867). A histidine residue in the N-terminal half of the molecule (region I) is an autophosphorylation site. Three additional motifs located in the C-terminal half of the molecule include an invariant asparagine residue in region II and two glycine-rich loops characteristic of nucleotide binding domains in regions III and IV. Recently a branched chain alpha-ketoacid dehydrogenase kinase has been found with characteristics of HPK in rat (Davie, supra).

[0317] Protein phosphatases regulate the effects of protein kinases by removing phosphate groups from molecules previously activated by kinases. The two principal categories of protein phosphatases are the protein (serine/threonine) phosphatases (PPs) and the protein tyrosine phosphatases (PTPs). PPs dephosphorylate phosphoserine/threonine residues and are important regulators of many cAMP-mediated hormone responses (Cohen, P. (1989) Annu. Rev. Biochem. 58:453-508). PTPs reverse the effects of protein tyrosine kinases and play a significant role in cell cycle and cell signaling processes (Charbonneau, supra). As previously noted, many PTKs are encoded by oncogenes, and oncogenesis is often accompanied by increased tyrosine phosphorylation activity. It is therefore possible that PTPs may prevent or reverse cell transformation and the growth of various cancers by controlling the levels of tyrosine phosphorylation in cells. This hypothesis is supported by studies showing that overexpression of PTPs can suppress transformation in cells, and that specific inhibition of PTPs can enhance cell transformation (Charbonneau, supra).

[0318] Phospholipid and Inositol-Phosphate Signaling

[0319] Inositol phospholipids (phosphoinositides) are involved in an intracellular signaling pathway that begins with binding of a signaling molecule to a G-protein linked receptor in the plasma membrane. This leads to the phosphorylation of phosphatidylinositol (PI) residues on the inner side of the plasma membrane to the biphosphate state (PIP₂) by inositol kinases. Simultaneously, the G-protein linked receptor binding stimulates a trimeric G-protein which in turn activates a phosphoinositide-specific phospholipase C-β. Phospholipase C-β then cleaves PIP₂ into two products, inositol triphosphate (IP₃) and diacylglycerol. These two products act as mediators for separate signaling events. IP₃ diffuses through the plasma membrane to induce calcium release from the endoplasmic reticulum (ER), while diacylglycerol remains in the membrane and helps activate protein kinase C, an STK that phosphorylates selected proteins in the target cell. The calcium response initiated by IP₃ is terminated by the dephosphorylation of IP₃ by specific inositol phosphatases. Cellular responses that are mediated by this pathway are glycogen breakdown in the liver in response to vasopressin, smooth muscle contraction in response to acetylcholine, and thrombin-induced platelet aggregation.

[0320] Cyclic Nucleotide Signaling

[0321] Cyclic nucleotides (cAMP and cGMP) function as intracellular second messengers to transduce a variety of extracellular signals including hormones, light, and neurotransmitters. In particular, cyclic-AMP dependent protein kinases (PKA) are thought to account for all of the effects of cAMP in most mammalian cells, including various hormone-induced cellular responses. Visual excitation and the phototransmission of light signals in the eye is controlled by cyclic-GMP regulated, Ca²⁺-specific channels. Because of the importance of cellular levels of cyclic nucleotides in mediating these various responses, regulating the synthesis and breakdown of cyclic nucleotides is an important matter. Thus adenylyl cyclase, which synthesizes cAMP from AMP, is activated to increase cAMP levels in muscle by binding of adrenaline to β-andrenergic receptors, while activation of guanylate cyclase and increased cGMP levels in photoreceptors leads to reopening of the Ca²⁺-specific channels and recovery of the dark state in the eye. In contrast, hydrolysis of cyclic nucleotides by cAMP and cGMP-specific phosphodiesterases (PDEs) produces the opposite of these and other effects mediated by increased cyclic nucleotide levels. PDEs appear to be particularly important in the regulation of cyclic nucleotides, considering the diversity found in this family of proteins. At least seven families of mammalian PDEs (PDE1-7) have been identified based on substrate specificity and affinity, sensitivity to cofactors, and sensitivity to inhibitory drugs (Beavo, J. A. (1995) Physiological Reviews 75:725-48). PDE inhibitors have been found to be particularly useful in treating various clinical disorders. Rolipram, a specific inhibitor of PDE4, has been used in the treatment of depression, and similar inhibitors are undergoing evaluation as anti-inflammatory agents. Theophylline is a nonspecific PDE inhibitor used in the treatment of bronchial asthma and other respiratory diseases (Banner, K. H. and C. P. Page (1995) Eur. Respir. J. 8:996-1000).

[0322] G-Protein Signaling

[0323] Guanine nucleotide binding proteins (G-proteins) are critical mediators of signal transduction between a particular class of extracellular receptors, the G-protein coupled receptors (GPCR), and intracellular second messengers such as cAMP and Ca²⁺. G-proteins are linked to the cytosolic side of a GPCR such that activation of the GPCR by ligand binding stimulates binding of the G-protein to GTP, inducing an “active” state in the G-protein. In the active state, the G-protein acts as a signal to trigger other events in the cell such as the increase of cAMP levels or the release of Ca²⁺ into the cytosol from the ER, which, in turn, regulate phosphorylation and activation of other intracellular proteins. Recycling of the G-protein to the inactive state involves hydrolysis of the bound GTP to GDP by a GTPase activity in the G-protein. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York N.Y., pp.734-759.) Two structurally distinct classes of G-proteins are recognized: heterotrimeric G-proteins, consisting of three different subunits, and monomeric, low molecular weight (LMW), G-proteins consisting of a single polypeptide chain.

[0324] The three polypeptide subunits of heterotrimeric G-proteins are the α, β, and γ subunits. The α subunit binds and hydrolyzes GTP. The β and γ subunits form a tight complex that anchors the protein to the inner side of the plasma membrane. The β subunits, also known as G-β proteins or β transducins, contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. Mutations and variant expression of β transducin proteins are linked with various disorders (Neer, E. J. et al. (1994) Nature 371:297-300; Margottin, F. et al. (1998) Mol. Cell 1:565-574).

[0325] LMW GTP-proteins are GTPases which regulate cell growth, cell cycle control, protein secretion, and intracellular vesicle interaction. They consist of single polypeptides which, like the α subunit of the heterotrimeric G-proteins, are able to bind and hydrolyze GTP, thus cycling between an inactive and an active state. At least sixty members of the LMW G-protein superfamily have been identified and are currently grouped into the six subfamilies of ras, rho, arf, sar1, ran, and rab. Activated ras genes were initially found in human cancers, and subsequent studies confirmed that ras function is critical in determining whether cells continue to grow or become differentiated. Other members of the LMW G-protein superfamily have roles in signal transduction that vary with the function of the activated genes and the locations of the G-proteins.

[0326] Guanine nucleotide exchange factors regulate the activities of LMW G-proteins by determining whether GTP or GDP is bound. GTPase-activating protein (GAP) binds to GTP-ras and induces it to hydrolyze GTP to GDP. In contrast, guanine nucleotide releasing protein (GNRP) binds to GDP-ras and induces the release of GDP and the binding of GTP.

[0327] Other regulators of G-protein signaling (RGS) also exist that act primarily by negatively regulating the G-protein pathway by an unknown mechanism (Druey, K. M. et al. (1996) Nature 379:742-746). Some 15 members of the RGS family have been identified. RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their ability to inhibit the interleukin (cytokine) induction of MAP kinase in cultured mammalian 293T cells (Druey, supra).

[0328] Calcium Signaling Molecules

[0329] Ca⁺² is another second messenger molecule that is even more widely used as an intracellular mediator than cAMP. Two pathways exist by which Ca⁺² can enter the cytosol in response to extracellular signals: One pathway acts primarily in nerve signal transduction where Ca⁺² enters a nerve terminal through a voltage-gated Ca⁺² channel. The second is a more ubiquitous pathway in which Ca⁺² is released from the ER into the cytosol in response to binding of an extracellular signaling molecule to a receptor. Ca²⁺ directly activates regulatory enzymes, such as protein kinase C, which trigger signal transduction pathways. Ca²⁺ also binds to specific Ca²⁺-binding proteins (CBPs) such as calmodulin (CaM) which then activate multiple target proteins in the cell including enzymes, membrane transport pumps, and ion channels. CaM interactions are involved in a multitude of cellular processes including, but not limited to, gene regulation, DNA synthesis, cell cycle progression, mitosis, cytokinesis, cytoskeletal organization, muscle contraction, signal transduction, ion homeostasis, exocytosis, and metabolic regulation (Celio, M. R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, Oxford, UK, pp. 15-20). Some CBPs can serve as a storage depot for Ca²⁺ in an inactive state. Calsequestrin is one such CBP that is expressed in isoforms specific to cardiac muscle and skeletal muscle. It is suggested that calsequestrin binds Ca²⁺ in a rapidly exchangeable state that is released during Ca²⁺-signaling conditions (Celio, M. R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, New York N.Y., pp. 222-224).

[0330] Cyclins

[0331] Cell division is the fundamental process by which all living things grow and reproduce. In most organisms, the cell cycle consists of three principle steps; interphase, mitosis, and cytokinesis. Interphase, involves preparations for cell division, replication of the DNA and production of essential proteins. In mitosis, the nuclear material is divided and separates to opposite sides of the cell. Cytokinesis is the final division and fission of the cell cytoplasm to produce the daughter cells.

[0332] The entry and exit of a cell from mitosis is regulated by the synthesis and destruction of a family of activating proteins called cyclins. Cyclins act by binding to and activating a group of cyclin-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins involved in the mitotic process. Several types of cyclins exist. (Ciechanover, A. (1994) Cell 79:13-21.) Two principle types are mitotic cyclin, or cyclin B, which controls entry of the cell into mitosis, and G1 cyclin, which controls events that drive the cell out of mitosis.

[0333] Signal Complex Scaffolding Proteins

[0334] Ceretain proteins in intracellular signaling pathways serve to link or cluster other proteins involved in the signaling cascade. A conserved protein domain called the PDZ domain has been identified in various membrane-associated signaling proteins. This domain has been implicated in receptor and ion channel clustering and in the targeting of multiprotein signaling complexes to specialized functional regions of the cytosolic face of the plasma membrane. (For a review of PDZ domain-containing proteins, see Ponting, C. P. et al. (1997) Bioessays 19:469-479.) A large proportion of PDZ domains are found in the eukaryotic MAGUK (membrane-associated guanylate kinase) protein family, members of which bind to the intracellular domains of receptors and channels. However, PDZ domains are also found in diverse membrane-localized proteins such as protein tyrosine phosphatases, serine/threonine kinases, G-protein cofactors, and synapse-associated proteins such as syntrophins and neuronal nitric oxide synthase (nNOS). Generally, about one to three PDZ domains are found in a given protein, although up to nine PDZ domains have been identified in a single protein.

[0335] Membrane Transport Molecules

[0336] SEQ ID NO:13 encodes, for example, a membrane transport molecule.

[0337] The plasma membrane acts as a barrier to most molecules. Transport between the cytoplasm and the extracellular environment, and between the cytoplasm and lumenal spaces of cellular organelles requires specific transport proteins. Each transport protein carries a particular class of molecule, such as ions, sugars, or amino acids, and often is specific to a certain molecular species of the class. A variety of human inherited diseases are caused by a mutation in a transport protein. For example, cystinuria is an inherited disease that results from the inability to transport cystine, the disulfide-linked dimer of cysteine, from the urine into the blood. Accumulation of cystine in the urine leads to the formation of cystine stones in the kidneys.

[0338] Transport proteins are multi-pass transmembrane proteins, which either actively transport molecules across the membrane or passively allow them to cross. Active transport involves directional pumping of a solute across the membrane, usually against an electrochemical gradient. Active transport is tightly coupled to a source of metabolic energy, such as ATP hydrolysis or an electrochemically favorable ion gradient. Passive transport involves the movement of a solute down its electrochemical gradient. Transport proteins can be further classified as either carrier proteins or channel proteins. Carrier proteins, which can function in active or passive transport, bind to a specific solute to be transported and undergo a conformational change which transfers the bound solute across the membrane. Channel proteins, which only function in passive transport, form hydrophilic pores across the membrane. When the pores open, specific solutes, such as inorganic ions, pass through the membrane and down the electrochemical gradient of the solute.

[0339] Carrier proteins which transport a single solute from one side of the membrane to the other are called uniporters. In contrast, coupled transporters link the transfer of one solute with simultaneous or sequential transfer of a second solute, either in the same direction (symport) or in the opposite direction (antiport). For example, intestinal and kidney epithelium contains a variety of symporter systems driven by the sodium gradient that exists across the plasma membrane. Sodium moves into the cell down its electrochemical gradient and brings the solute into the cell with it. The sodium gradient that provides the driving force for solute uptake is maintained by the ubiquitous Na⁺/K⁺ ATPase. Sodium-coupled transporters include the mammalian glucose transporter (SGLT1), iodide transporter (NIS), and multivitamin transporter (SMVT). All three transporters have twelve putative transmembrane segments, extracellular glycosylation sites, and cytoplasmically-oriented N- and C-termini. NIS plays a crucial role in the evaluation, diagnosis, and treatment of various thyroid pathologies because it is the molecular basis for radioiodide thyroid-imaging techniques and for specific targeting of radioisotopes to the thyroid gland (Levy, O. et al. (1997) Proc. Natl. Acad. Sci. USA 94:5568-5573). SMVT is expressed in the intestinal mucosa, kidney, and placenta, and is implicated in the transport of the water-soluble vitamins, e.g., biotin and pantothenate (Prasad, P. D. et al. (1998) J. Biol. Chem. 273:7501-7506).

[0340] Transporters play a major role in the regulation of pH, excretion of drugs, and the cellular K⁺/Na⁺ balance. Monocarboxylate anion transporters are proton-coupled symporters with a broad substrate specificity that includes L-lactate, pyruvate, and the ketone bodies acetate, acetoacetate, and beta-hydroxybutyrate. At least seven isoforms have been identified to date. The isoforms are predicted to have twelve transmembrane (TM) helical domains with a large intracellular loop between TM6 and TM7, and play a critical role in maintaining intracellular pH by removing the protons that are produced stoichiometrically with lactate during glycolysis. The best characterized H(+)-monocarboxylate transporter is that of the erythrocyte membrane, which transports L-lactate and a wide range of other aliphatic monocarboxylates. Other cells possess H(+)-linked monocarboxylate transporters with differing substrate and inhibitor selectivities. In particular, cardiac muscle and tumor cells have transporters that differ in their K_(m) values for certain substrates, including stereoselectivity for L- over D-lactate, and in their sensitivity to inhibitors. There are Na(+)-monocarboxylate cotransporters on the luminal surface of intestinal and kidney epithelia, which allow the uptake of lactate, pyruvate, and ketone bodies in these tissues. In addition, there are specific and selective transporters for organic cations and organic anions in organs including the kidney, intestine and liver. Organic anion transporters are selective for hydrophobic, charged molecules with electron-attracting side groups. Organic cation transporters, such as the ammonium transporter, mediate the secretion of a variety of drugs and endogenous metabolites, and contribute to the maintenance of intercellular pH. (Poole, R. C. and A. P. Halestrap (1993) Am. J. Physiol. 264:C761-C782; Price, N. T. et al. (1998) Biochem. J. 329:321-328; and Martinelle, K. and I. Haggstrom (1993) J. Biotechnol. 30: 339-350.)

[0341] The largest and most diverse family of transport proteins known is the ATP-binding cassette (ABC) transporters. As a family, ABC transporters can transport substances that differ markedly in chemical structure and size, ranging from small molecules such as ions, sugars, amino acids, peptides, and phospholipids, to lipopeptides, large proteins, and complex hydrophobic drugs. ABC proteins consist of four modules: two nucleotide-binding domains (NBD), which hydrolyze ATP to supply the energy required for transport, and two membrane-spanning domains (MSD), each containing six putative transmembrane segments. These four modules may be encoded by a single gene, as is the case for the cystic fibrosis transmembrane regulator (CFTR), or by separate genes. When:encoded by separate genes, each gene product contains a single NBD and MSD. These “half-molecules” form homo- and heterodimers, such as Tap1 and Tap2, the endoplasmic reticulum-based major histocompatibility (MHC) peptide transport system. Several genetic diseases are attributed to defects in ABC transporters, such as the following diseases and their corresponding proteins: cystic fibrosis (CFTR, an ion channel), adrenoleukodystrophy (adrenoleukodystrophy protein, ALDP), Zellweger syndrome (peroxisomal membrane protein-70, PMP70), and hyperinsulinemic hypoglycemia (sulfonylurea receptor, SUR). Overexpression of the multidrug resistance (MDR) protein, another ABC transporter, in human cancer cells makes the cells resistant to a variety of cytotoxic drugs used in chemotherapy (Taglight, D. and S. Michaelis (1998) Meth. Enzymol. 292:131-163).

[0342] Transport of fatty acids across the plasma membrane can occur by diffusion, a high capacity, low affinity process. However, under normal physiological conditions a significant fraction of fatty acid transport appears to occur via a high affinity, low capacity protein-mediated transport process. Fatty acid transport protein (FATP), an integral membrane protein with four transmembrane segments, is expressed in tissues exhibiting high levels of plasma membrane fatty acid flux, such as muscle, heart, and adipose. Expression of FATP is upregulated in 3T3-L1 cells during adipose conversion, and expression in COS7 fibroblasts elevates uptake of long-chain fatty acids (Hui, T. Y. et al. (1998) J. Biol. Chem. 273:27420-27429).

[0343] Ion Channels

[0344] The electrical potential of a cell is generated and maintained by controlling the movement of ions across the plasma membrane. The movement of ions requires ion channels, which form an ion-selective pore within the membrane. There are two basic types of ion channels, ion transporters and gated ion channels. Ion transporters utilize the energy obtained from ATP hydrolysis to actively transport an ion against the ion's concentration gradient. Gated ion channels allow passive flow of an ion down the ion's electrochemical gradient under restricted conditions. Together, these types of ion channels generate, maintain, and utilize an electrochemical gradient that is used in 1) electrical impulse conduction down the axon of a nerve cell, 2) transport of molecules into cells against concentration gradients, 3) initiation of muscle contraction, and 4) endocrine cell secretion.

[0345] Ion transporters generate and maintain the resting electrical potential of a cell. Utilizing the energy derived from ATP hydrolysis, they transport ions against the ion's concentration gradient. These transmembrane ATPases are divided into three families. The phosphorylated (P) class ion transporters, including Na⁺-K⁺ ATPase, Ca²⁺-ATPase, and H+-ATPase, are activated by a phosphorylation event. P-class ion transporters are responsible for maintaining resting potential distributions such that cytosolic concentrations of Na⁺ and Ca²⁺ are low and cytosolic concentration of K⁺ is high. The vacuolar (V) class of ion transporters includes H⁺ pumps on intracellular organelles, such as lysosomes and Golgi. V-class ion transporters are responsible for generating the low pH within the lumen of these organelles that is required for function. The coupling factor (F) class consists of H⁺ pumps in the mitochondria. F-class ion transporters utilize a proton gradient to generate ATP from ADP and inorganic phosphate (P_(i)).

[0346] The resting potential of the cell is utilized in many processes involving carrier proteins and gated ion channels. Carrier proteins utilize the resting potential to transport molecules into and out of the cell. Amino acid and glucose transport into many cells is linked to sodium ion co-transport (symport) so that the movement of Na⁺ down an electrochemical gradient drives transport of the other molecule up a concentration gradient. Similarly, cardiac muscle links transfer of Ca²⁺ out of the cell with transport of Na⁺ into the cell (antiport).

[0347] Ion channels share common structural and mechanistic themes. The channel consists of four or five subunits or protein monomers that are arranged like a barrel in the plasma membrane. Each subunit typically consists of six potential transmembrane segments (S1, S2, S3, S4, S5, and S6). The center of the barrel forms a pore lined by α-helices or β-strands. The side chains of the amino acid residues comprising the α-helices or β-strands establish the charge (cation or anion) selectivity of the channel. The degree of selectivity, or what specific ions are allowed to pass through the channel, depends on the diameter of the narrowest part of the pore.

[0348] Gated ion channels control ion flow by regulating the opening and closing of pores. These channels are categorized according to the manner of regulating the gating function. Mechanically-gated channels open pores in response to mechanical stress, voltage-gated channels open pores in response to changes in membrane potential, and ligand-gated channels open pores in the presence of a specific ion, nucleotide, or neurotransmitter.

[0349] Voltage-gated Na⁺ and K⁺ channels are necessary for the function of electrically excitable cells, such as nerve and muscle cells. Action potentials, which lead to neurotransmitter release and muscle contraction, arise from large, transient changes in the permeability of the membrane to Na⁺ and K⁺ ions. Depolarization of the membrane beyond the threshold level opens voltage-gated Na⁺ channels. Sodium ions flow into the cell, further depolarizing the membrane and opening more voltage-gated Na⁺ channels, which propagates the depolarization down the length of the cell. Depolarization also opens voltage-gated potassium channels. Consequently, potassium ions flow outward, which leads to repolarization of the membrane. Voltage-gated channels utilize charged residues in the fourth transmembrane segment (S4) to sense voltage change. The open state lasts only about 1 millisecond, at which time the channel spontaneously converts into an inactive state that cannot be opened irrespective of the membrane potential. Inactivation is mediated by the channel's N-terminus, which acts as a plug that closes the pore. The transition from an inactive to a closed state requires a return to resting potential.

[0350] Voltage-gated Na⁺ channels are heterotrimeric complexes composed of a 260 kDa pore forming α subunit that associates with two smaller auxiliary subunits, β1 and β2. The β2 subunit is an integral membrane glycoprotein that contains an extracellular Ig domain, and its association with α and β1 subunits correlates with increased functional expression of the channel, a change in its gating properties, and an increase in whole cell capacitance due to an increase in membrane surface area. (Isom, L. L. et al. (1995) Cell 83:433-442.)

[0351] Voltage-gated Ca²⁺ channels are involved in presynaptic neurotransmitter release, and heart and skeletal muscle contraction. The voltage-gated Ca²⁺ channels from skeletal muscle (L-type) and brain (N-type) have been purified, and though their functions differ dramatically, they have similar subunit compositions. The channels are composed of three subunits. The α₁ subunit forms the membrane pore and voltage sensor, while the α₂δ and β subunits modulate the voltage-dependence, gating properties, and the current amplitude of the channel. These subunits are encoded by at least six α₁, one α₂δ, and four β genes. A fourth subunit, γ, has been identified in skeletal muscle. (Walker, D. et al. (1998) J. Biol. Chem. 273:2361-2367; and Jay, S. D. et al. (1990) Science 248:490-492.)

[0352] Chloride channels are necessary in endocrine secretion and in regulation of cytosolic and organelle pH. In secretory epithelial cells, Cl⁻ enters the cell across a basolateral membrane through. an Na⁺, K⁺/Cl⁻ cotransporter, accumulating in the cell above its electrochemical equilibrium concentration. Secretion of Cl⁻ from the apical surface, in response to hormonal stimulation, leads to flow of Na⁺ and water into the secretory lumen. The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel encoded by the gene for cystic fibrosis, a common fatal genetic disorder in humans. Loss of CFTR function decreases transepithelial water secretion and, as a result, the layers of mucus that coat the respiratory tree, pancreatic ducts, and intestine are dehydrated and difficult to clear. The resulting blockage of these sites leads to pancreatic insufficiency, “meconium ileus”, and devastating “chronic obstructive pulmonary disease” (Al-Awqati, Q. et al. (1992) J. Exp. Biol. 172:245-266).

[0353] Many intracellular organelles contain H⁺-ATPase pumps that generate transmembrane pH and electrochemical differences by moving protons from the cytosol to the organelle lumen. If the membrane of the organelle is permeable to other ions, then the electrochemical gradient can be abrogated without affecting the pH differential. In fact, removal of the electrochemical barrier allows more H⁺ to be pumped across the membrane, increasing the pH differential. Cl⁻ is the sole counterion of H⁺ translocation in a number of organelles, including chromaffin granules, Golgi vesicles, lysosomes, and endosomes. Functions that require a low vacuolar pH include uptake of small molecules such as biogenic amines in chromaffin granules, processing of vacuolar constituents such as pro-hormones by proteolytic enzymes, and protein degradation in lysosomes (Al-Awqati, supra).

[0354] Ligand-gated channels open their pores when an extracellular or intracellular mediator binds to the channel. Neurotransmitter-gated channels are channels that open when a neurotransmitter binds to their extracellular domain. These channels exist in the postsynaptic membrane of nerve or muscle cells. There are two types of neurotransmitter-gated channels. Sodium channels open in response to excitatory neurotransmitters, such as acetylcholine, glutamate, and serotonin. This opening causes an. influx of Na⁺ and produces the initial localized depolarization that activates the voltage-gated channels and starts the action potential. Chloride channels open in response to inhibitory neurotransmitters, such as γ-aminobutyric acid (GABA) and glycine, leading to hyperpolarization of the membrane and the subsequent generation of an action potential.

[0355] Ligand-gated channels can be regulated by intracellular second messengers. Calcium-activated K⁺ channels are gated by internal calcium ions. In nerve cells, an influx of calcium during depolarization opens K⁺ channels to modulate the magnitude of the action potential (Ishi, T. M. et al. (1997) Proc. Natl. Acad. Sci. USA 94:11651-11656). Cyclic nucleotide-gated (CNG) channels are gated by cytosolic cyclic nucleotides. The best examples of these are the cAMP-gated Na⁺ channels involved in olfaction and the cGMP-gated cation channels involved in vision. Both systems involve ligand-mediated activation of a G-protein coupled receptor which then alters the level of cyclic nucleotide within the cell.

[0356] Ion channels are expressed in a number of tissues where they are implicated in a variety of processes. CNG channels, while abundantly expressed in photoreceptor and olfactory sensory cells, are also found in kidney, lung, pineal, retinal ganglion cells, testis, aorta, and brain. Calcium-activated K⁺ channels may be responsible for the vasodilatory effects of bradykinin in the kidney and for shunting excess K⁺ from brain capillary endothelial cells into the blood. They are also implicated in repolarizing granulocytes after agonist-stimulated depolarization (Ishi, supra). Ion channels have been the target for many drug therapies. Neurotransmitter-gated channels have been targeted in therapies for treatment of insomnia, anxiety, depression, and schizophrenia. Voltage-gated channels have been targeted in therapies for arrhythmia, ischemic stroke, head trauma, and neurodegenerative disease (Taylor, C. P. and L. S. Narasimhan (1997) Adv. Pharmacol. 39:47-98).

[0357] Disease Correlation

[0358] The etiology of numerous human diseases and disorders can be attributed to defects in the transport of molecules across membranes. Defects in the trafficking of membrane-bound transporters and ion channels are associated with several disorders, e.g. cystic fibrosis, glucose-galactose malabsorption syndrome, hypercholesterolemia, von Gierke disease, and certain forms of diabetes mellitus. Single-gene defect diseases resulting in an inability to transport small molecules across membranes include, e.g., cystinuria, iminoglycinuria, Hartup disease, and Fanconi disease (van't Hoff, W. G. (1996) Exp. Nephrol. 4:253-262; Talente, G. M. et al. (1994) Ann. Intern. Med. 120:218-226; and Chillon, M. et al. (1995) New Engl. J. Med. 332:1475-1480).

[0359] Protein Modification and Maintenance Molecules

[0360] The cellular processes regulating modification and maintenance of protein molecules coordinate their conformation, stabilization, and degradation. Each of these processes is mediated by key enzymes or proteins such as proteases, protease inhibitors, transferases, isomerases, and molecular chaperones.

[0361] Proteases

[0362] Proteases cleave proteins and peptides at the peptide bond that forms the backbone of the peptide and protein chain. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Typical protein half-lives range from hours to a few days, so that within all living cells, precursor proteins are being cleaved to their active form, signal sequences proteolytically removed from targeted proteins, and aged or defective proteins degraded by proteolysis. Proteases function in bacterial, parasitic, and viral invasion and replication within a host. Four principal categories of mammalian proteases have been identified based on active site structure, mechanism of action, and overall three-dimensional structure. (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 1-5).

[0363] The serine proteases (SPs) have a serine residue, usually within a conserved sequence, in an active site composed of the serine, an aspartate, and a histidine residue. SPs include the digestive enzymes trypsin and chymotrypsin, components of the complement cascade and the blood-clotting cascade, and enzymes that control extracellular protein degradation. The main SP sub-families are trypases, which cleave after arginine or lysine; aspartases, which cleave after aspartate; chymases, which cleave after phenylalanine or leucine; metases, which cleavage after methionine; and serases which cleave after serine. Enterokinase, the initiator of intestinal digestion, is a serine protease found in the intestinal brush border, where it cleaves the acidic propeptide from trypsinogen to yield active trypsin (Kitamoto, Y. et al. (1994) Proc. Natl. Acad. Sci. USA 91:7588-7592). Prolylcarboxypeptidase, a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des-Arg9] bradykinin, shares sequence homology with members of both the serine carboxypeptidase and prolylendopeptidase families (Tan, F. et al. (1993) J. Biol. Chem. 268:16631-16638).

[0364] Cysteine proteases (CPs) have a cysteine as the major catalytic residue at an active site where catalysis proceeds via an intermediate thiol ester and is facilitated by adjacent histidine and aspartic acid residues. CPs are involved in diverse cellular processes ranging from the processing of precursor proteins to intracellular degradation. Mammalian CPs include lysosomal cathepsins and cytosolic calcium activated proteases, calpains. CPs are produced by monocytes, macrophages and other cells of the immune system which migrate to sites of inflammation and secrete molecules involved in tissue repair. Overabundance of these repair molecules plays a role in certain disorders. In autoimmune diseases such as rheumatoid arthritis, secretion of the cysteine peptidase cathepsin C degrades collagen, laminin, elastin and other structural proteins found in the extracellular matrix of bones.

[0365] Aspartic proteases are members of the cathepsin family of lysosomal proteases and include pepsin A, gastricsin, chymosin, renin, and cathepsins D and E. Aspartic proteases have a pair of aspartic acid residues in the active site, and are most active in the pH 2-3 range, in which one of the aspartate residues is ionized, the other un-ionized. Aspartic proteases include bacterial penicillopepsin, mammalian pepsin, renin, chymosin, and certain fungal proteases. Abnormal regulation and expression of cathepsins is evident in various inflammatory disease states. In cells isolated from inflamed synovia, the mRNA for stromelysin, cytokines, TIMP-1, cathepsin, gelatinase, and other molecules is preferentially expressed. Expression of cathepsins L and D is elevated in synovial tissues from patients with rheumatoid arthritis and osteoarthritis. Cathepsin L expression may also contribute to the influx of mononuclear cells which exacerbates the destruction of the rheumatoid synovium. (Keyszer, G. M. (1995) Arthritis Rheum. 38:976-984.) The increased expression and differential regulation of the cathepsins are linked to the metastatic potential of a variety of cancers and as such are of therapeutic and prognostic interest (Chambers, A. F. et al. (1993) Crit. Rev. Oncog. 4:95-114).

[0366] Metalloproteases have active sites that include two glutamic acid residues and one histidine residue that serve as binding sites for zinc. Carboxypeptidases A and B are the principal mammalian metalloproteases. Both are exoproteases of similar structure and active sites. Carboxypeptidase A, like chymotrypsin, prefers C-terminal aromatic and aliphatic side chains of hydrophobic nature, whereas carboxypeptidase B is directed toward basic arginine and lysine residues. Glycoprotease (GCP), or O-sialoglycoprotein endopeptidase, is a metallopeptidase which specifically cleaves O-sialoglycoproteins such as glycophorin A. Another metallopeptidase, placental leucine aminopeptidase (P-LAP) degrades several peptide hormones such as oxytocin and vasopressin, suggesting a role in maintaining homeostasis during pregnancy, and is expressed in several tissues (Rogi, T. et al. (1996) J. Biol. Chem. 271:56-61).

[0367] Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction; transcriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183).

[0368] Signal Peptidases

[0369] The mechanism for the translocation process into the endoplasmic reticulum (ER) involves the recognition of an N-terminal signal peptide on the elongating protein. The signal peptide directs the protein and attached ribosome to a receptor on the ER membrane. The polypeptide chain passes through a pore in the ER membrane into the lumen while the N-terminal signal peptide remains attached at the membrane surface. The process is completed when signal peptidase located inside the ER cleaves the signal peptide from the protein and releases the protein into the lumen.

[0370] Protease Inhibitors

[0371] Protease inhibitors and other regulators of protease activity control the activity and effects of proteases. Protease inhibitors have been shown to control pathogenesis in animal models of proteolytic disorders (Murphy, G. (1991) Agents Actions Suppl. 35:69-76). Low levels of the cystatins, low molecular weight inhibitors of the cysteine proteases, correlate with malignant progression of tumors. (Calkins, C. et al (1995) Biol. Biochem. Hoppe Seyler 376:71-80). Serpins are inhibitors of mammalian plasma serine proteases. Many serpins serve to regulate the blood clotting cascade and/or the complement cascade in mammals. Sp32 is a positive regulator of the mammalian acrosomal protease, acrosin, that binds the proenzyme, proacrosin, and thereby aides in packaging the enzyme into the acrosomal matrix (Baba, T. et al. (1994) J. Biol. Chem. 269:10133-10140). The Kunitz family of serine protease inhibitors are characterized by one or more “Kunitz domains” containing a series of cysteine residues that are regularly spaced over approximately 50 amino acid residues and form three intrachain disulfide bonds. Members of this family include aprotinin, tissue factor pathway inhibitor (TFPI-1 and TFPI-2), inter-α-trypsin inhibitor, and bikunin. (Marlor, C. W. et al. (1997) J. Biol. Chem. 272:12202-12208.) Members of this family are potent inhibitors (in the nanomolar range) against serine proteases such as kallikrein and plasmin. Aprotinin has clinical utility in reduction of perioperative blood loss.

[0372] A major portion of all proteins synthesized in eukaryotic cells are synthesized on the cytosolic surface of the endoplasmic reticulum (ER). Before these immature proteins are distributed to other organelles in the cell or are secreted, they must be transported into the interior lumen of the ER where post-translational modifications are performed. These modifications include protein folding and the formation of disulfide bonds, and N-linked glycosylations.

[0373] Protein Isomerases

[0374] Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form intramolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imidic bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R. E. et al. (1984) Science 226: 544-547).

[0375] Protein Glycosylation

[0376] The glycosylation of most soluble secreted and membrane-bound proteins by oligosaccharides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase. Although the exact purpose of this “N-linked” glycosylation is unknown, the presence of oligosaccharides tends to make a glycoprotein resistant to protease digestion. In addition, oligosaccharides attached to cell-surface proteins called selectins are known to function in cell-cell adhesion processes (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Co., New York N.Y., p.608). “O-linked” glycosylation of proteins also occurs in the ER by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalysed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W. H. Freeman and Co., New York N.Y., pp.700-708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface.

[0377] An additional glycosylation mechanism operates in the ER specifically to target lysosomal enzymes to lysosomes and prevent their secretion. Lysosomal enzymes in the ER receive an N-linked oligosaccharide, like plasma membrane and secreted proteins, but are then phosphorylated on one or two mannose residues. The phosphorylation of mannose residues occurs in two steps, the first step being the addition of an N-acetylglucosamine phosphate residue by N-acetylglucosamine phosphotransferase, and the second the removal of the N-acetylglucosamine group by phosphodiesterase. The phosphorylated mannose residue then targets the lysosomal enzyme to a mannose 6-phosphate receptor which transports it to a lysosome vesicle (Lodish, supra, pp. 708-711).

[0378] Chaperones

[0379] Molecular chaperones are proteins that aid in the proper folding of immature proteins and refolding of improperly folded ones, the assembly of protein subunits, and in the transport of unfolded proteins across membranes. Chaperones are also called heat-shock proteins (hsp) because of their tendency to be expressed in dramatically increased amounts following brief exposure of cells to elevated temperatures. This latter property most likely reflects their need in the refolding of proteins that have become denatured by the high temperatures. Chaperones may be divided into several classes according to their location, function, and molecular weight, and include hsp60, TCP1, hsp70, hsp40 (also called DnaJ), and hsp90. For example, hsp90 binds to steroid hormone receptors, represses transcription in the absence of the ligand, and provides proper folding of the ligand-binding domain of the receptor in the presence of the hormone (Burston, S. G. and A. R. Clarke (1995) Essays Biochem. 29:125-136). Hsp60 and hsp70 chaperones aid in the transport and folding of newly synthesized proteins. Hsp70 acts early in protein folding, binding a newly synthesized protein before it leaves the ribosome and transporting the protein to the mitochondria or ER before releasing the folded protein. Hsp60 , along with hsp10, binds misfolded proteins and gives them the opportunity to refold correctly. All chaperones share an affinity for hydrophobic patches on incompletely folded proteins and the ability to hydrolyze ATP. The energy of ATP hydrolysis is used to release the hsp-bound protein in its properly folded state (Alberts, supra, pp 214, 571-572).

[0380] Nucleic Acid Synthesis and Modification Molecules

[0381] SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:20 encode, for example, nucleic acid synthesis and modification molecules.

[0382] Polymerases

[0383] DNA and RNA replication are critical processes for cell replication and function. DNA and RNA replication are mediated by the enzymes DNA and RNA polymerase, respectively, by a “templating” process in which the nucleotide sequence of a DNA or RNA strand is copied by complementary base-pairing into a complementary nucleic acid sequence of either DNA or RNA. However, there are fundamental differences between the two processes.

[0384] DNA polymerase catalyzes the stepwise addition of a deoxyribonucleotide to the 3′-OH end of a polynucleotide strand (the primer strand) that is paired to a second (template) strand. The new DNA strand therefore grows in the 5′ to 3′ direction (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., pp. 251-254). The substrates for the polymerization reaction are the corresponding deoxynucleotide triphosphates which must base-pair with the correct nucleotide on the template strand in order to be recognized by the polymerase. Because DNA exists as a double-stranded helix, each of the two strands may serve as a template for the formation of a new complementary strand. Each of the two daughter cells of the dividing cell therefore inherits a new DNA double helix containing one old and one new strand. Thus, DNA is said to be replicated “semiconservatively” by DNA polymerase. In addition to the synthesis of new DNA, DNA polymerase is also involved in the repair of damaged DNA as discussed below under “Ligases.”

[0385] In contrast to DNA polymerase, RNA polymerase uses a DNA template strand to “transcribe” DNA into RNA using ribonucleotide triphosphates as substrates. Like DNA polymerization, RNA polymerization proceeds in a 5′ to 3′ direction by addition of a ribonucleoside monophosphate to the 3′-OH end of a growing RNA chain. DNA transcription generates messenger RNAs (mRNA) that carry information for protein synthesis, as well as the transfer, ribosomal, and other RNAs that have structural or catalytic functions. In eukaryotes, three discrete RNA polymerases synthesize the three different types of RNA (Alberts, supra, pp. 367-368). RNA polymerase I makes the large ribosomal RNAs, RNA polymerase II makes the mRNAs that will be translated into proteins, and RNA polymerase III makes a variety of small, stable RNAs, including 5S ribosomal RNA and the transfer RNAs (tRNA). In all cases, RNA synthesis is initiated by binding of the RNA polymerase to a promoter region on the DNA and synthesis begins at a start site within the promoter. Synthesis is completed at a broad, general stop or termination region in the DNA where both the polymerase and the completed RNA chain are released.

[0386] Ligases

[0387] DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA are corrected before replication or transcription of the DNA can occur. Because of the efficiency of the DNA repair process, fewer than one in one thousand accidental base changes causes a mutation (Alberts, supra, pp. 245-249). The three steps common to most types of DNA repair are (1) excision of the damaged or altered base or nucleotide by DNA nucleases, leaving a gap; (2) insertion of the correct nucleotide in this gap by DNA polymerase using the complementary strand as the template; and (3) sealing the break left between the inserted nucleotide(s) and the existing DNA strand by DNA ligase. In the last reaction, DNA ligase uses the energy from ATP hydrolysis to activate the 5′ end of the broken phosphodiester bond before forming the new bond with the 3′-OH of the DNA strand. In Bloom's syndrome, an inherited human disease, individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, supra, p. 247).

[0388] Nucleases

[0389] Nucleases comprise both enzymes that hydrolyze DNA (DNase) and RNA (RNase). They serve different purposes in nucleic acid metabolism. Nucleases hydrolyze the phosphodiester bonds between adjacent nucleotides either at internal positions (endonucleases) or at the terminal 3′ or 5′ nucleotide positions (exonucleases). A DNA exonuclease activity in DNA polymerase, for example, serves to remove improperly paired nucleotides attached to the 3′-OH end of the growing DNA strand by the polymerase and thereby serves a “proofreading” function. As mentioned above, DNA endonuclease activity is involved in the excision step of the DNA repair process.

[0390] RNases also serve a variety of functions. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5′ end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral replication cycle. Pancreatic RNase secreted by the pancreas into the intestine hydrolyzes RNA present in ingested foods. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, C. H. (1997) Nat. Biotechnol. 15:529-536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections.

[0391] Methylases

[0392] Methylation of specific nucleotides occurs in both DNA and RNA, and serves different functions in the two macromolecules. Methylation of cytosine residues to form 5-methyl cytosine in DNA occurs specifically at CG sequences which are base-paired with one another in the DNA double-helix. This pattern of methylation is passed from generation to generation during DNA replication by an enzyme called “maintenance methylase” that acts preferentially on those CG sequences that are base-paired with a CG sequence that is already methylated. Such methylation appears to distinguish active from inactive genes by preventing the binding of regulatory proteins that “turn on” the gene, but permit the binding of proteins that inactivate the gene (Alberts, supra, pp. 448-451). In RNA metabolism, “tRNA methylase” produces one of several nucleotide modifications in tRNA that affect the conformation and base-pairing of the molecule and facilitate the recognition of the appropriate mRNA codons by specific tRNAs. The primary methylation pattern is the dimethylation of guanine residues to form N,N-dimethyl guanine.

[0393] Helicases and Single-Stranded Binding Proteins

[0394] Helicases are enzymes that destabilize and unwind double helix structures in both DNA and RNA. Since DNA replication occurs more or less simultaneously on both strands, the two strands must first separate to generate a replication “fork” for DNA polymerase to act on. Two types of replication proteins contribute to this process, DNA helicases and single-stranded binding proteins. DNA helicases hydrolyze ATP and use the energy of hydrolysis to separate the DNA strands. Single-stranded binding proteins (SSBs) then bind to the exposed DNA strands without covering the bases, thereby temporarily stabilizing them for templating by the DNA polymerase (Alberts, supra, pp. 255-256).

[0395] RNA helicases also alter and regulate RNA conformation and secondary structure. Like the DNA helicases, RNA helicases utilize energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis. Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblastoma (Nb) and retinoblastoma (Rb) tumors (Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168). These observations suggest that DDX1 may promote or enhance tumor progression by altering the normal secondary structure and expression levels of RNA in cancer cells. Other DEAD-box helicases have been implicated either directly or indirectly in tumorigenesis (Discussed in Godbout, supra). For example, murine p68 is mutated in ultraviolet light-induced tumors, and human DDX6 is located at a chromosomal breakpoint associated with B-cell lymphoma. Similarly, a chimeric protein comprised of DDX10 and NUP98, a nucleoporin protein, may be involved in the pathogenesis of certain myeloid malignancies.

[0396] Topoisomerases

[0397] Besides the need to separate DNA strands prior to replication, the two strands must be “unwound” from one another prior to their separation by DNA helicases. This function is performed by proteins known as DNA topoisomerases. DNA topoisomerase effectively acts as a reversible nuclease that hydrolyzes a phosphodiesterase bond in a DNA strand, permitting the two strands to rotate freely about one another to remove the strain of the helix, and then rejoins the original phosphodiester bond between the two strands. Two types of DNA topoisomerase exist, types I and II. DNA Topoisomerase I causes a single-strand break in a DNA helix to allow the rotation of the two strands of the helix about the remaining phosphodiester bond in the opposite strand. DNA topoisomerase II causes a transient break in both strands of a DNA helix where two double helices cross over one another. This type of topoisomerase can efficiently separate two interlocked DNA circles (Alberts, supra, pp.260-262). Type II topoisomerases are largely confined to proliferating cells in eukaryotes, such as cancer cells. For this reason they are targets for anticancer drugs. Topoisomerase II has been implicated in multi-drug resistance (MDR) as it appears to aid in the repair of DNA damage inflicted. by DNA binding agents such as doxorubicin and vincristine.

[0398] Recombinases

[0399] Genetic recombination is the process of rearranging DNA sequences within an organism's genome to provide genetic variation for the organism in response to changes in the environment. DNA recombination allows variation in the particular combination of genes present in an individual's genome, as well as the timing and level of expression of these genes (see Alberts, supra, pp. 263-273). Two broad classes of genetic recombination are commonly recognized, general recombination and site-specific recombination. General recombination involves genetic exchange between any homologous pair of DNA sequences usually located on two copies of the same chromosome. The process is aided by enzymes called recombinases that “nick” one strand of a DNA duplex more or less randomly and permit exchange with the complementary strand of another duplex. The process does not normally change the arrangement of genes on a chromosome. In site-specific recombination, the recombinase recognizes specific nucleotide sequences present in one or both of the recombining molecules. Base-pairing is not involved in this form of recombination and therefore does not require DNA homology between the recombining molecules. Unlike general recombination, this form of recombination can alter the relative positions of nucleotide sequences in chromosomes.

[0400] Splicing Factors

[0401] Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5′ end with methylguanosine, polyadenylating the 3′ end, and splicing to remove introns. The primary RNA transcript from DNA is a faithful copy of the gene containing both exon and intron sequences, and the latter sequences must be cut out of the RNA transcript to produce an mRNA that codes for a protein. This “splicing” of the mRNA sequence takes place in the nucleus with the aid of a large, multicomponent ribonucleoprotein complex known as a spliceosome. The spliceosomal complex is composed of five small nuclear ribonucleoprotein particles (snRNPs) designated U1, U2, U4, U5, and U6, and a number of additional proteins. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base pair with intron consensus sequences. The protein components mediate spliceosome assembly and the splicing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry, W. H. Freeman and Company, New York N.Y., p. 863).

[0402] Adhesion Molecules

[0403] SEQ ID NO:21 and SEQ ID NO:22 encode, for example, adhesion molecules.

[0404] The surface of a cell is rich in transmembrane proteoglycans, glycoproteins, glycolipids, and receptors. These macromolecules mediate adhesion with other cells and with components of the extracellular matrix (ECM). The interaction of the cell with its surroundings profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways controlling cell proliferation and differentiation, tissue construction, and embryonic development.

[0405] Cadherins

[0406] Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all solid tissues of multicellular organisms. These proteins share multiple repeats of a cadherin-specific motif, and the repeats form the folding units of the cadherin extracellular domain. Cadherin molecules cooperate to form focal contacts, or adhesion plaques, between adjacent epithelial cells. The cadherin family includes the classical cadherins and protocadherins. Classical cadherins include the E-cadherin, N-cadherin, and P-cadherin subfamilies. E-cadherin is present on many types of epithelial cells and is especially important for embryonic development. N-cadherin is present on nerve, muscle, and lens cells and is also critical for embryonic development. P-cadherin is present on cells of the placenta and epidermis. Recent studies report that protocadherins are involved in a variety of cell-cell interactions (Suzuki, S. T. (1996) J. Cell Sci. 109:2609-2611). The intracellular anchorage of cadherins is regulated by their dynamic association with catenins, a family of cytoplasmic signal transduction proteins associated with the actin cytoskeleton. The anchorage of cadherins to the actin cytoskeleton appears to be regulated by protein tyrosine phosphorylation, and the cadherins are the target of phosphorylation-induced junctional disassembly (Aberle, H. et al. (1996) J. Cell. Biochem. 61:514-523).

[0407] Integrins

[0408] Integrins are ubiquitous transmembrane adhesion molecules that link the ECM to the internal cytoskeleton. Integrins are composed of two noncovalently associated transmembrane glycoprotein subunits called α and β. Integrins function as receptors that play a role in signal transduction. For example, binding of integrin to its extracellular ligand may stimulate changes in intracellular calcium levels or protein kinase activity (Sjaastad, M. D. and W. J. Nelson (1997) BioEssays 19:47-55). At least ten cell surface receptors of the integrin family recognize the ECM component fibronectin, which is involved in many different biological processes including cell migration and embryogenesis (Johansson, S. et al. (1997) Front. Biosci. 2:D126-D146).

[0409] Lectins

[0410] Lectins comprise a ubiquitous family of extracellular glycoproteins which bind cell surface carbohydrates specifically and reversibly, resulting in the agglutination of cells (reviewed in Drickamer, K. and M. E. Taylor (1993) Annu. Rev. Cell Biol. 9:237-264). This function is particularly important for activation of the immune response. Lectins mediate the agglutination and mitogenic stimulation of lymphocytes at sites of inflammation (Lasky, L. A. (1991) J. Cell. Biochem. 45:139-146; Paietta, E. et al. (1989) J. Immunol. 143:2850-2857).

[0411] Lectins are further classified into subfamilies based on carbohydrate-binding specificity and other criteria. The galectin subfamily, in particular, includes lectins that bind β-galactoside carbohydrate moieties in a thiol-dependent manner (reviewed in Hadari, Y. R. et al. (1998) J. Biol. Chem. 270:3447-3453). Galectins are widely expressed and developmentally regulated. Because all galectins lack an N-terminal signal peptide, it is suggested that galectins are externalized through an atypical secretory mechanism. Two classes of galectins have been defined based on molecular weight and oligomerization properties. Small galectins form homodimers and are about 14 to 16 kilodaltons in mass, while large galectins are monomeric and about 29-37 kilodaltons.

[0412] Galectins contain a characteristic carbohydrate recognition domain (CRD). The CRD is about 140 amino acids and contains several stretches of about 1-10 amino acids which are highly conserved among all galectins. A particular 6-amino acid motif within the CRD contains conserved tryptophan and arginine residues which are critical for carbohydrate binding. The CRD of some galectins also contains cysteine residues which may be important for disulfide bond formation. Secondary structure predictions indicate that the CRD forms several β-sheets.

[0413] Galectins play a number of roles in diseases and conditions associated with cell-cell and cell-matrix interactions. For example, certain galectins associate with sites of inflammation and bind to cell surface immunoglobulin E molecules. In addition, galectins may play an important role in cancer metastasis. Galectin overexpression is correlated with the metastatic potential of cancers in humans and mice. Moreover, anti-galectin antibodies inhibit processes associated with cell transformation, such as cell aggregation and anchorage-independent growth (See, for example, Su, Z.-Z. et al. (1996) Proc. Natl. Acad. Sci. USA 93:7252-7257).

[0414] Selectins

[0415] Selectins, or LEC—CAMs, comprise a specialized lectin subfamily involved primarily in inflammation and leukocyte adhesion (Reviewed in Lasky, supra). Selectins mediate the recruitment of leukocytes from the circulation to sites of acute inflammation and are expressed on the surface of vascular endothelial cells in response to cytokine signaling. Selectins bind to specific ligands on the leukocyte cell membrane and enable the leukocyte to adhere to and migrate along the endothelial surface. Binding of selectin to its ligand leads to polarized rearrangement of the actin cytoskeleton and stimulates signal transduction within the leukocyte (Brenner, B. et al. (1997) Biochem. Biophys. Res. Commun. 231:802-807; Hidari, K. I. et al. (1997) J. Biol. Chem. 272:28750-28756). Members of the selectin family possess three characteristic motifs: a lectin or carbohydrate recognition domain; an epidermal growth factor-like domain; and a variable number of short consensus repeats (scr or “sushi” repeats) which are also present in complement regulatory proteins. The selectins include lymphocyte adhesion molecule-1 (Lam-1 or L-selectin), endothelial leukocyte adhesion molecule-1 (ELAM-1 or E-selectin), and granule membrane protein-140 (GMP-140 or Pβ-selectin) (Johnston, G. I. et al. (1989) Cell 56:1033-1044).

[0416] Antigen Recognition Molecules

[0417] All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal, and parasitic infections. A key feature of the immune system is its ability to distinguish foreign molecules, or antigens, from “self” molecules. This ability is mediated primarily by secreted and transmembrane proteins expressed by leukocytes (white blood cells) such as lymphocytes, granulocytes, and monocytes. Most of these proteins belong to the immunoglobulin (Ig) superfamily, members of which contain one or more repeats of a conserved structural domain. This Ig domain is comprised of antiparallel β sheets joined by a disulfide bond in an arrangement called the Ig fold. Members of the Ig superfamily include T-cell receptors, major histocompatibility (MHC) proteins, antibodies, and immune cell-specific surface markers such as CD4, CD8, and CD28.

[0418] MHC proteins are cell surface markers that bind to and present foreign antigens to T cells. MHC molecules are classified as either class I or class II. Class I MHC molecules (MHC I) are expressed on the surface of almost all cells and are involved in the presentation of antigen to cytotoxic T cells. For example, a cell infected with virus will degrade intracellular viral proteins and express the protein fragments bound to MHC I molecules on the cell surface. The MHC I/antigen complex is recognized by cytotoxic T-cells which destroy the infected cell and the virus within. Class II MHC molecules are expressed primarily on specialized antigen-presenting cells of the immune system, such as B-cells and macrophages. These cells ingest foreign proteins from the extracellular fluid and express MHC II/antigen complex on the cell surface. This complex activates helper T-cells, which then secrete cytokines and other factors that stimulate the immune response. MHC molecules also play an important role in organ rejection following transplantation. Rejection occurs when the recipient's T-cells respond to foreign MHC molecules on the transplanted organ in the same way as to self MHC molecules bound to foreign antigen. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, New York N.Y., pp. 1229-1246.)

[0419] Antibodies, or immunoglobulins, are either expressed on the surface of B-cells or secreted by B-cells into the circulation. Antibodies bind and neutralize foreign antigens in the blood and other extracellular fluids. The prototypical antibody is a tetramer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds. This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, IgE, IgG and IgM, are defined by the α, δ, ε, γ, and μ H-chain types. There are two types of L-chains, κ and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tetrameric, while the other classes of antibodies are generally variants or multimers of this basic structure.

[0420] H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant region. The constant region consists of about 110 amino acids in L-chains and about 330 or 440 amino acids in H-chains. The amino acid sequence of the constant region is nearly identical among H- or L-chains of a particular class. The variable region consists of about 110 amino acids in both H- and L-chains. However, the amino acid sequence of the variable region differs among H- or L-chains of a particular class. Within each H- or L-chain variable region are three hypervariable regions of extensive sequence diversity, each consisting of about 5 to 10 amino acids. In the antibody molecule, the H- and L-chain hypervariable regions come together to form the antigen recognition site. (Reviewed in Alberts, supra, pp. 1206-1213 and 1216-1217.)

[0421] Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region.

[0422] The immune system is capable of recognizing and responding to any foreign molecule that enters the body. Therefore, the immune system must be armed with a full repertoire of antibodies against all potential antigens. Such antibody diversity is generated by somatic rearrangement of gene segments encoding variable and constant regions. These gene segments are joined together by site-specific recombination which occurs between highly conserved DNA sequences that flank each gene segment. Because there are hundreds of different gene segments, millions of unique genes can be generated combinatorially. In addition, imprecise joining of these segments and an unusually high rate of somatic mutation within these segments further contribute to the generation of a diverse antibody population.

[0423] T-cell receptors are both structurally and functionally related to antibodies. (Reviewed in Alberts, supra, pp. 1228-1229.) T-cell receptors are cell surface proteins that bind foreign antigens and mediate diverse aspects of the immune response. A typical T-cell receptor is a heterodimer comprised of two disulfide-linked polypeptide chains called α and β. Each chain is about 280 amino acids in length and contains one variable region and one constant region. Each variable or constant region folds into an Ig domain. The variable regions from the α and β chains come together in the heterodimer to form the antigen recognition site. T-cell receptor diversity is generated by somatic rearrangement of gene segments encoding the α and β chains. T-cell receptors recognize small peptide antigens that are expressed on the surface of antigen-presenting cells and pathogen-infected cells. These peptide antigens are presented on the cell surface in association with major histocompatibility proteins which provide the proper context for antigen recognition.

[0424] Secreted and Extracellular Matrix Molecules

[0425] SEQ ID NO:25 encodes, for example, a secreted/extracellular matrix molecule.

[0426] Protein secretion is essential for cellular function. Protein secretion is mediated by a signal peptide located at the amino terminus of the protein to be secreted. The signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane. Secreted proteins are often synthesized as inactive precursors that are activated by post-translational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secreted proteins with amino terminal signal peptides include receptors, extracellular matrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of The Cell, Garland Publishing, New York N.Y., pp. 557-560, 582-592.)

[0427] The extracellular matrix (ECM) is a complex network of glycoproteins, polysaccharides, proteoglycans, and other macromolecules that are secreted from the cell into the extracellular space. The ECM remains in close association with the cell surface and provides a supportive meshwork that profoundly influences cell shape, motility, strength, flexibility, and adhesion. In fact, adhesion of a cell to its surrounding matrix is required for cell survival except in the case of metastatic tumor cells, which have overcome the need for cell-ECM anchorage. This phenomenon suggests that the ECM plays a critical role in the molecular mechanisms of growth control and metastasis. (Reviewed in Ruoslahti, E. (1996) Sci. Am. 275:72-77.) Furthermore, the ECM determines the structure and physical properties of connective tissue and is particularly important for morphogenesis and other processes associated with embryonic development and pattern formation.

[0428] The collagens comprise a family of ECM proteins that provide structure to bone, teeth, skin, ligaments, tendons, cartilage, blood vessels, and basement membranes. Multiple collagen proteins have been identified. Three collagen molecules fold together in a triple helix stabilized by interchain disulfide bonds. Bundles of these triple helices then associate to form fibrils. Collagen primary structure consists of hundreds of (Gly-X-Y) repeats where about a third of the X and Y residues are Pro. Glycines are crucial to helix formation as the bulkier amino acid sidechains cannot fold into the triple helical conformation. Because of these strict sequence requirements, mutations in collagen genes have severe consequences. Osteogenesis imperfecta patients have brittle bones that fracture easily; in severe cases patients die in utero or at birth. Ehlers-Danlos syndrome patients have hyperelastic skin, hypermobile joints, and susceptibility to aortic and intestinal rupture. Chondrodysplasia patients have short stature and ocular disorders. Alport syndrome patients have hematuria, sensorineural deafness, and eye lens deformation. (Isselbacher, K. J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York N.Y., pp. 2105-2117; and Creighton, T. E. (1984) Proteins, Structures and Molecular Principles, W. H. Freeman and Company, New York N.Y., pp. 191-197.)

[0429] Elastin and related proteins confer elasticity to tissues such as skin, blood vessels, and lungs. Elastin is a highly hydrophobic protein of about 750 amino acids that is rich in proline and glycine residues. Elastin molecules are highly cross-linked, forming an extensive extracellular network of fibers and sheets. Elastin fibers are surrounded by a sheath of microfibrils which are composed of a number of glycoproteins, including fibrillin. Mutations in the gene encoding fibrillin are responsible for Marfan's syndrome, a genetic disorder characterized by defects in connective tissue. In severe cases, the aortas of afflicted individuals are prone to rupture. (Reviewed in Alberts, supra, pp. 984-986.)

[0430] Fibronectin is a large ECM glycoprotein found in all vertebrates. Fibronectin exists as a dimer of two subunits, each containing about 2,500 amino acids. Each subunit folds into a rod-like structure containing multiple domains. The domains each contain multiple repeated modules, the most common of which is the type III fibronectin repeat. The type III fibronectin repeat is about 90 amino acids in length and is also found in other ECM proteins and in some plasma membrane and cytoplasmic proteins. Furthermore, some type III fibronectin repeats contain a characteristic tripeptide consisting of Arginine-Glycine-Aspartic acid (RGD). The RGD sequence is recognized by the integrin family of cell surface receptors and is also found in other ECM proteins. Disruption of both copies of the gene encoding fibronectin causes early embryonic lethality in mice. The mutant embryos display extensive morphological defects, including defects in the formation of the notochord, somites, heart, blood vessels, neural tube, and extraembryonic structures. (Reviewed in Alberts, supra, pp. 986-987.)

[0431] Laminin is a major glycoprotein component of the basal lamina which underlies and supports epithelial cell sheets. Laminin is one of the first ECM proteins synthesized in the developing embryo. Laminin is an 850 kilodalton protein composed of three polypeptide chains joined in the shape of a cross by disulfide bonds. Laminin is especially important for angiogenesis and in particular, for guiding the formation of capillaries. (Reviewed in Alberts, supra, pp. 990-991.)

[0432] There are many other types of proteinaceous ECM components, most of which can be classified as proteoglycans. Proteoglycans are composed of unbranched polysaccharide chains (glycosaminoglycans) attached to protein cores. Common proteoglycans include aggrecan, betaglycan, decorin, perlecan, serglycin, and syndecan-1. Some of these molecules not only provide mechanical support, but also bind to extracellular signaling molecules, such as fibroblast growth factor and transforming growth factor β, suggesting a role for proteoglycans in cell-cell communication and cell growth. (Reviewed in Alberts, supra, pp. 973-978.) Likewise, the glycoproteins tenascin-C and tenascin-R are expressed in developing and lesioned neural tissue and provide stimulatory and anti-adhesive (inhibitory) properties, respectively, for axonal growth. (Faissner, A. (1997) Cell Tissue Res. 290:331-341.)

[0433] Cytoskeletal Molecules

[0434] SEQ ID NO:26 and SEQ ID NO:27 encode, for example, cytoskeletal molecules.

[0435] The cytoskeleton is a cytoplasmic network of protein fibers that mediate cell shape, structure, and movement. The cytoskeleton supports the cell membrane and forms tracks along which organelles and other elements move in the cytosol. The cytoskeleton is a dynamic structure that allows cells to adopt various shapes and to carry out directed movements. Major cytoskeletal fibers include the microtubules, the microfilaments, and the intermediate filaments. Motor proteins, including myosin, dynein, and kinesin, drive movement of or along the fibers. The motor protein dynamin drives the formation of membrane vesicles. Accessory or associated proteins modify the structure or activity of the fibers while cytoskeletal membrane anchors connect the fibers to the cell membrane.

[0436] Tubulins

[0437] Microtubules, cytoskeletal fibers with a diameter of about 24 nm, have multiple roles in the cell. Bundles of microtubules form cilia and flagella, which are whip-like extensions of the cell membrane that are necessary for sweeping materials across an epithelium and for swimming of sperm, respectively. Marginal bands of microtubules in red blood cells and platelets are important for these cells' pliability. Organelles, membrane vesicles, and proteins are transported in the cell along tracks of microtubules. For example, microtubules run through nerve cell axons, allowing bi-directional transport of materials and membrane vesicles between the cell body and the nerve terminal. Failure to supply the nerve terminal with these vesicles blocks the transmission of neural signals. Microtubules are also critical to chromosomal movement during cell division. Both stable and short-lived populations of microtubules exist in the cell.

[0438] Microtubules are polymers of GTP-binding tubulin protein subunits. Each subunit is a heterodimer of α- and β-tubulin, multiple isoforms of which exist. The hydrolysis of GTP is linked to the addition of tubulin subunits at the end of a microtubule. The subunits interact head to tail to form protofilaments; the protofilaments interact side to side to form a microtubule. A microtubule is polarized, one end ringed with α-tubulin and the other with β-tubulin, and the two ends differ in their rates of assembly. Generally, each microtubule is composed of 13 protofilaments although 11 or 15 protofilament-microtubules are sometimes found. Cilia and flagella contain doublet microtubules. Microtubules grow from specialized structures known as centrosomes or microtubule-organizing centers (MTOCs). MTOCs may contain one or two centrioles, which are pinwheel arrays of triplet microtubules. The basal body, the organizing center located at the base of a cilium or flagellum, contains one centriole. Gamma tubulin present in the MTOC is important for nucleating the polymerization of α- and P- tubulin heterodimers but does not polymerize into microtubules.

[0439] Microtubule-Associated Proteins

[0440] Microtubule-associated proteins (MAPs) have roles in the assembly and stabilization of microtubules. One major family of MAPs, assembly MAPs, can be identified in neurons as well as non-neuronal cells. Assembly MAPs are responsible for cross-linking microtubules in the cytosol. These MAPs are organized into two domains: a basic microtubule-binding domain and an acidic projection domain. The projection domain is the binding site for membranes, intermediate filaments, or other microtubules. Based on sequence analysis, assembly MAPs can be further grouped into two types: Type I and Type II. Type I MAPs, which include MAP1A and MAP1B, are large, filamentous molecules that co-purify with microtubules and are abundantly expressed in brain and testes. Type I MAPs contain several repeats of a positively-charged amino acid sequence motif that binds and neutralizes negatively charged tubulin, leading to stabilization of microtubules. MAP1A and MAP1B are each derived from a single precursor polypeptide that is subsequently proteolytically processed to generate one heavy chain and one light chain.

[0441] Another light chain, LC3, is a 16.4 kDa molecule that binds MAP1A, MAP1B, and microtubules. It is suggested that LC3 is synthesized from a source other than the MAP1A or MAP1B transcripts, and that the expression of LC3 may be important in regulating the microtubule binding activity of MAP1A and MAP1B during cell proliferation (Mann, S. S. et al. (1994) J. Biol. Chem. 269:11492-11497).

[0442] Type II MAPs, which include MAP2a, MAP2b, MAP2c, MAP4, and Tau, are characterized by three to four copies of an 18-residue sequence in the microtubule-binding domain. MAP2a, MAP2b, and MAP2c are found only in dendrites, MAP4 is found in non-neuronal cells, and Tau is found in axons and dendrites of nerve cells. Alternative splicing of the Tau mRNA leads to the existence of multiple forms of Tau protein. Tau phosphorylation is altered in neurodegenerative disorders such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia and Parkinsonism linked to chromosome 17. The altered Tau phosphorylation leads to a collapse of the microtubule network and the formation of intraneuronal Tau aggregates (Spillantini, M. G. and M. Goedert (1998) Trends Neurosci. 21:428-433).

[0443] The protein pericentrin is found in the MTOC and has a role in microtubule assembly.

[0444] Actins

[0445] Microfilaments, cytoskeletal filaments with a diameter of about 7-9 nm, are vital to cell locomotion, cell shape, cell adhesion, cell division, and muscle contraction. Assembly and disassembly of the microfilaments allow cells to change their morphology. Microfilaments are the polymerized form of actin, the most abundant intracellular protein in the eukaryotic cell. Human cells contain six isoforms of actin. The three α-actins are found in different kinds of muscle, nonmuscle β-actin and nonmuscle γ-actin are found in nonmuscle cells, and another γ-actin is found in intestinal smooth muscle cells. G-actin, the monomeric form of actin, polymerizes into polarized, helical F-actin filaments, accompanied by the hydrolysis of ATP to ADP. Actin filaments associate to form bundles and networks, providing a framework to support the plasma membrane and determine cell shape. These bundles and networks are connected to the cell membrane. In muscle cells, thin filaments containing actin slide past thick filaments containing the motor protein myosin during contraction. A family of actin-related proteins exist that are not part of the actin cytoskeleton, but rather associate with microtubules and dynein.

[0446] Actin-Associated Proteins

[0447] Actin-associated proteins have roles in cross-linking, severing, and stabilization of actin filaments and in sequestering actin monomers. Several of the actin-associated proteins have multiple functions. Bundles and networks of actin filaments are held together by actin cross-linking proteins. These proteins have two actin-binding sites, one for each filament. Short cross-linking proteins promote bundle formation while longer, more flexible cross-linking proteins promote network formation. Calmodulin-like calcium-binding domains in actin cross-linking proteins allow calcium regulation of cross-linking. Group I cross-linking proteins have unique actin-binding domains and include the 30 kD protein, EF-1a, fascin, and scruin. Group II cross-linking proteins have a 7,000-MW actin-binding domain and include villin and dematin. Group III cross-linking proteins have pairs of a 26,000-MW actin-binding domain and include fimbrin, spectrin, dystrophin, ABP 120, and filamin.

[0448] Severing proteins regulate the length of actin filaments by breaking them into short pieces or by blocking their ends. Severing proteins include gCAP39, severin (fragmin), gelsolin, and villin. Capping proteins can cap the ends of actin filaments, but cannot break filaments. Capping proteins include CapZ and tropomodulin. The proteins thymosin and profilin sequester actin monomers in the cytosol, allowing a pool of unpolymerized actin to exist. The actin-associated proteins tropomyosin, troponin, and caldesmon regulate muscle contraction in response to calcium.

[0449] Intermediate Filaments and Associated Proteins

[0450] Intermediate filaments (IFs) are cytoskeletal fibers with a diameter of about 10 nm, intermediate between that of microfilaments and microtubules. IFs serve structural roles in the cell, reinforcing cells and organizing cells into tissues. IFs are particularly abundant in epidermal cells and in neurons. IFs are extremely stable, and, in contrast to microfilaments and microtubules, do not function in cell motility.

[0451] Five types of IF proteins are known in mammals. Type I and Type II proteins are the acidic and basic keratins, respectively. Heterodimers of the acidic and basic keratins are the building blocks of keratin IFs. Keratins are abundant in soft epithelia such as skin and cornea, hard epithelia such as nails and hair, and in epithelia that line internal body cavities. Mutations in keratin genes lead to epithelial diseases including epidermolysis bullosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, pachyonychia congenita, and white sponge nevus. Some of these diseases result in severe skin blistering. (See, e.g., Wawersik, M. et al. (1997) J. Biol. Chem. 272:32557-32565; and Corden L. D. and W. H. McLean (1996) Exp. Dermatol. 5:297-307.)

[0452] Type III IF proteins include desmin, glial fibrillary acidic protein, vimentin, and peripherin. Desmin filaments in muscle cells link myofibrils into bundles and stabilize sarcomeres in contracting muscle. Glial fibrillary acidic protein filaments are found in the glial cells that surround neurons and astrocytes. Vimentin filaments are found in blood vessel endothelial cells, some epithelial cells, and mesenchymal cells such as fibroblasts, and are commonly associated with microtubules. Vimentin filaments may have roles in keeping the nucleus and other organelles in place in the cell. Type IV IFs include the neurofilaments and nestin. Neurofilaments, composed of three polypeptides NF-L, NF-M, and NF-H, are frequently associated with microtubules in axons. Neurofilaments are responsible for the radial growth and diameter of an axon, and ultimately for the speed of nerve impulse transmission.

[0453] Changes in phosphorylation and metabolism of neurofilaments are observed in neurodegenerative diseases including amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease (Julien, J. P. and W. E. Mushynski (1998) Prog. Nucleic Acid Res. Mol. Biol. 61:1-23). Type V IFs, the lamins, are found in the nucleus where they support the nuclear membrane.

[0454] IFs have a central α-helical rod region interrupted by short nonhelical linker segments. The rod region is bracketed, in most cases, by non-helical head and tail domains. The rod regions of intermediate filament proteins associate to form a coiled-coil dimer. A highly ordered assembly process leads from the dimers to the IFs. Neither ATP nor GTP is needed for IF assembly, unlike that of microfilaments and microtubules.

[0455] IF-associated proteins (IFAPs) mediate the interactions of IFs with one another and with other cell structures. IFAPs cross-link IFs into a bundle, into a network, or to the plasma membrane, and may cross-link IFs to the microfilament and microtubule cytoskeleton. Microtubules and IFs are in particular closely associated. IFAPs include BPAG1, plakoglobin, desmoplakin I, desmoplakin II, plectin, ankyrin, filaggrin, and lamin B receptor.

[0456] Cytoskeletal-Membrane Anchors

[0457] Cytoskeletal fibers are attached to the plasma membrane by specific proteins. These attachments are important for maintaining cell shape and for muscle contraction. In erythrocytes, the spectrin-actin cytoskeleton is attached to cell membrane by three proteins, band 4.1, ankyrin, and adducin. Defects in this attachment result in abnormally shaped cells which are more rapidly degraded by the spleen, leading to anemia. In platelets, the spectrin-actin cytoskeleton is also linked to the membrane by ankyrin; a second actin network is anchored to the membrane by filamin. In muscle cells the protein dystrophin links actin filaments to the plasma membrane; mutations in the dystrophin gene lead to Duchenne muscular dystrophy. In adherens junctions and adhesion plaques the peripheral membrane proteins α-actinin and vinculin attach actin filaments to the cell membrane.

[0458] IFs are also attached to membranes by cytoskeletal-membrane anchors. The nuclear lamina is attached to the inner surface of the nuclear membrane by the lamin B receptor. Vimentin IFs are attached to the plasma membrane by ankyrin and plectin. Desmosome and hemidesmosome membrane junctions hold together epithelial cells of organs and skin. These membrane junctions allow shear forces to be distributed across the entire epithelial cell layer, thus providing strength and rigidity to the epithelium. IFs in epithelial cells are attached to the desmosome by plakoglobin and desmoplakins. The proteins that link IFs to hemidesmosomes are not known. Desmin IFs surround the sarcomere in muscle and are linked to the plasma membrane by paranemin, synemin, and ankyrin.

[0459] Myosin-related Motor Proteins

[0460] Myosins are actin-activated ATPases, found in eukaryotic cells, that couple hydrolysis of ATP with motion. Myosin provides the motor function for muscle contraction and intracellular movements such as phagocytosis and rearrangement of cell contents during mitotic cell division (cytokinesis). The contractile unit of skeletal muscle, termed the sarcomere, consists of highly ordered arrays of thin actin-containing filaments and thick myosin-containing filaments. Crossbridges form between the thick and thin filaments, and the ATP-dependent movement of myosin heads within the thick filaments pulls the thin filaments, shortening the sarcomere and thus the muscle fiber.

[0461] Myosins are composed of one or two heavy chains and associated light chains. Myosin heavy chains contain an amino-terminal motor or head domain, a neck that is the site of light-chain binding, and a carboxy-terminal tail domain. The tail domains may associate to form an α-helical coiled coil. Conventional myosins, such as those found in muscle tissue, are composed of two myosin heavy-chain subunits, each associated with two light-chain subunits that bind at the neck region and play a regulatory role. Unconventional myosins, believed to function in intracellular motion, may contain either one or two heavy chains and associated light chains. There is evidence for about 25 myosin heavy chain genes in vertebrates, more than half of them unconventional.

[0462] Dynein-related Motor Proteins

[0463] Dyneins are (−) end-directed motor proteins which act on microtubules. Two classes of dyneins, cytosolic and axonemal, have been identified. Cytosolic dyneins are responsible for translocation of materials along cytoplasmic microtubules, for example, transport from the nerve terminal to the cell body and transport of endocytic vesicles to lysosomes. Cytoplasmic dyneins are also reported to play a role in mitosis. Axonemal dyneins are responsible for the beating of flagella and cilia. Dynein on one microtubule doublet walks along the adjacent microtubule doublet. This sliding force produces bending forces that cause the flagellum or cilium to beat. Dyneins have a native mass between 1000 and 2000 kDa and contain either two or three force-producing heads driven by the hydrolysis of ATP. The heads are linked via stalks to a basal domain which is composed of a highly variable number of accessory intermediate and light chains.

[0464] Kinesin-related Motor Proteins

[0465] Kinesins are (+) end-directed motor proteins which act on microtubules. The prototypical kinesin molecule is involved in the transport of membrane-bound vesicles and organelles. This function is particularly important for axonal transport in neurons. Kinesin is also important in all cell types for the transport of vesicles from the Golgi complex to the endoplasmic reticulum. This role is critical for maintaining the identity and functionality of these secretory organelles.

[0466] Kinesins define a ubiquitous, conserved family of over 50 proteins that can be classified into at least 8 subfamilies based on primary amino acid sequence, domain structure, velocity of movement, and cellular function. (Reviewed in Moore, J. D. and S. A. Endow (1996) Bioessays 18:207-219; and Hoyt, A. M. (1994) Curr. Opin. Cell Biol. 6:63-68.) The prototypical kinesin molecule is a heterotetramer comprised of two heavy polypeptide chains (KHCs) and two light polypeptide chains (KLCs). The KHC subunits are typically referred to as “kinesin.” KHC is about 1000 amino acids in length, and KLC is about 550 amino acids in length. Two KHCs dimerize to form a rod-shaped molecule with three distinct regions of secondary structure. At one end of the molecule is a globular motor domain that functions in ATP hydrolysis and microtubule binding. Kinesin motor domains are highly conserved and share over 70% identity. Beyond the motor domain is an α-helical coiled-coil region which mediates dimerization. At the other end of the molecule is a fan-shaped tail that associates with molecular cargo. The tail is formed by the interaction of the KHC C-termini with the two KLCs.

[0467] Members of the more divergent subfamilies of kinesins are called kinesin-related proteins (KRPs), many of which function during mitosis in eukaryotes (Hoyt, supra). Some KRPs are required for assembly of the mitotic spindle. In vivo and in vitro analyses suggest that these KRPs exert force on microtubules that comprise the mitotic spindle, resulting in the separation of spindle poles. Phosphorylation of KRP is required for this activity. Failure to assemble the mitotic spindle results in abortive mitosis and chromosomal aneuploidy, the latter condition being characteristic of cancer cells. In addition, a unique KRP, centromere protein E, localizes to the kinetochore of human mitotic chromosomes and may play a role in their segregation to opposite spindle poles.

[0468] Dynamin-related Motor Proteins

[0469] Dynamin is a large GTPase motor protein that functions as a “molecular pinchase,” generating a mechanochemical force used to sever membranes. This activity is important in forming clathrin-coated vesicles from coated pits in endocytosis and in the biogenesis of synaptic vesicles in neurons. Binding of dynamin to a membrane leads to dynamin's self-assembly into spirals that may act to constrict a flat membrane surface into a tubule. GTP hydrolysis induces a change in conformation of the dynamin polymer that pinches the membrane tubule, leading to severing of the membrane tubule and formation of a membrane vesicle. Release of GDP and inorganic phosphate leads to dynamin disassembly. Following disassembly the dynamin may either dissociate from the membrane or remain associated to the vesicle and be transported to another region of the cell. Three homologous dynamin genes have been discovered, in addition to several dynamin-related proteins. Conserved dynamin regions are the N-terminal GTP-binding domain, a central pleckstrin homology domain that binds membranes, a central coiled-coil region that may activate dynamin's GTPase activity, and a C-terminal proline-rich domain that contains several motifs that bind SH3 domains on other proteins. Some dynamin-related proteins do not contain the pleckstrin homology domain or the proline-rich domain. (See McNiven, M. A. (1998) Cell 94:151-154; Scaife, R. M. and R. L. Margolis (1997) Cell. Signal. 9:395-401.)

[0470] The cytoskeleton is reviewed in Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y.

[0471] Ribosomal Molecules

[0472] SEQ ID NO:30 and SEQ ID NO:31 encode, for example, ribosomal molecules.

[0473] Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate messenger RNA into polypeptides. The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Ribosomal protein activities include binding rRNA and organizing the conformation of the junctions between rRNA helices (Woodson, S. A. and N. B. Leontis (1998) Curr. Opin. Struct. Biol. 8:294-300; Ramakrishnan, V. and S. W. White (1998) Trends Biochem. Sci. 23:208-212.) Three important sites are identified on the ribosome. The aminoacyl-tRNA site (A site) is where charged tRNAs (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (The ribosome is reviewed in Stryer, L. (1995) Biochemistry W. H. Freeman and Company, New York N.Y., pp. 888-908; and Lodish, H. et al. (1995) Molecular Cell Biology Scientific American Books, New York N.Y. pp. 119-138.)

[0474] Chromatin Molecules

[0475] The nuclear DNA of eukaryotes is organized into chromatin. Two types of chromatin are observed: euchromatin, some of which may be transcribed, and heterochromatin so densely packed that much of it is inaccessible to transcription. Chromatin packing thus serves to regulate protein expression in eukaryotes. Bacteria lack chromatin and the chromatin-packing level of gene regulation.

[0476] The fundamental unit of chromatin is the nucleosome of 200 DNA base pairs associated with two copies each of histones H2A, H2B, H3, and H4. Adjascent nucleosomes are linked by another class of histones, H1. Low molecular weight non-histone proteins called the high mobility group (HMG), associated with chromatin, may function in the unwinding of DNA and stabilization of single-stranded DNA. Chromodomain proteins function in compaction of chromatin into its transcriptionally silent heterochromatin form.

[0477] During mitosis, all DNA is compacted into heterochromatin and transcription ceases. Transcription in interphase begins with the activation of a region of chromatin. Active chromatin is decondensed. Decondensation appears to be accompanied by changes in binding coefficient, phosphorylation and acetylation states of chromatin histones. HMG proteins HMG13 and HMG17 selectively bind activated chromatin. Topoisomerases remove superhelical tension on DNA. The activated region decondenses, allowing gene regulatory proteins and transcription factors to assemble on the DNA.

[0478] Patterns of chromatin structure can be stably inherited, producing heritable patterns of gene expression. In mammals, one of the two X chromosomes in each female cell is inactivated by condensation to heterochromatin during zygote development. The inactive state of this chromosome is inherited, so that adult females are mosaics of clusters of paternal-X and maternal-X clonal cell groups. The condensed X chromosome is reactivated in meiosis.

[0479] Chromatin is associated with disorders of protein expression such as thalassemia, a genetic anemia resulting from the removal of the locus control region (LCR) required for decondensation of the globin gene locus.

[0480] For a review of chromatin structure and function see Alberts, B. et al. (1994) Molecular Cell Biology, third edition, Garland Publishing, Inc., New York N.Y., pp. 351-354, 433-439.

[0481] Electron Transfer Associated Molecules

[0482] SEQ ID NO:23 and SEQ ID NO:24 encode, for example, electron transfer associated molecules.

[0483] Electron carriers such as cytochromes accept electrons from NADH or FADH₂ and donate them to other electron carriers. Most electron-transferring proteins, except ubiquinone, are prosthetic groups such as flavins, heme, FeS clusters, and copper, bound to inner membrane proteins. Adrenodoxin, for example, is an FeS protein that forms a complex with NADPH:adrenodoxin reductase and cytochrome p450. Cytochromes contain a heme prosthetic group, a porphyrin ring containing a tightly bound iron atom. Electron transfer reactions play a crucial role in cellular energy production.

[0484] Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted to pyruvate in the cytoplasm. Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to CO₂ coupled by enzymes to the transport of electrons from NADH and FADH₂ to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P_(i).

[0485] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO₂ with concomitant formation of NADH, FADH₂, and GTP. In oxidative phosphorylation, the transfer of electrons from NADH and FADH₂ to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P_(i) by the F₀F₁ ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F₀F₁ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c₁, FeS protein, and cytochrome c oxidase.

[0486] ATP synthesis requires membrane transport enzymes including the phosphate transporter and the ATP-ADP antiport protein. The ATP-binding casette (ABC) superfamily has also been suggested as belonging to the mitochondrial transport group (Hogue, D. L. et al. (1999) J. Mol. Biol. 285:379-389). Brown fat uncoupling protein dissipates oxidative energy as heat, and may be involved the fever response to infection and trauma (Cannon, B. et al. (1998) Ann. NY Acad. Sci. 856:171-187).

[0487] Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of transport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells.

[0488] Mitochondria contain a small amount of DNA. Human mitochondrial DNA encodes 13 proteins, 22 tRNAs, and 2 rRNAs. Mitochondrial-DNA encoded proteins include NADH-Q reductase, a cytochrome reductase subunit, cytochrome oxidase subunits, and ATP synthase subunits.

[0489] Electron-transfer reactions also occur outside the mitochondria in locations such as the endoplasmic reticulum, which plays a crucial role in lipid and protein biosynthesis. Cytochrome b5 is a central electron donor for various reductive reactions occurring on the cytoplasmic surface of liver endoplasmic reticulum. Cytochrome b5 has been found in Golgi, plasma, endoplasmic reticulum (ER), and microbody membranes.

[0490] For a review of mitochondrial metabolism and regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York N.Y., pp. 745-797 and Stryer (1995) Biochemistry, W. H. Freeman and Co., San Francisco Calif., pp 529-558, 988-989.

[0491] The majority of mitochondrial proteins are encoded by nuclear genes, are synthesized on cytosolic ribosomes, and are imported into the mitochondria. Nuclear-encoded proteins which are destined for the mitochondrial matrix typically contain positively-charged amino terminal signal sequences. Import of these preproteins from the cytoplasm requires a multisubunit protein complex in the outer membrane known as the translocase of outer mitochondrial membrane (TOM; previously designated MOM; Pfanner, N. et al. (1996) Trends Biochem. Sci. 21:51-52) and at least three inner membrane proteins which comprise the ranslocase of inner mitochondrial membrane (TIM; previously designated MIM; Pfanner, supra). An inside-negative membrane potential across the inner mitochondrial membrane is also required for preprotein import. Preproteins are recognized by surface receptor components of the TOM complex and are translocated through a proteinaceous pore formed by other TOM components. Proteins targeted to the matrix are then recognized by the import machinery of the TIM complex. The import systems of the outer and inner membranes can function independently (Segui-Real, B. et al. (1993) EMBO J. 12:2211-2218).

[0492] Once precursor proteins are in the mitochondria, the leader peptide is cleaved by a signal peptidase to generate the mature protein. Most leader peptides are removed in a one step process by a protease termed mitochondrial processing peptidase (MPP) (Paces, V. et al. (1993) Proc. Natl. Acad. Sci. USA 90:5355-5358). In some cases a two-step process occurs in which MPP generates an intermediate precursor form which is cleaved by a second enzyme, mitochondrial intermediate peptidase, to generate the mature protein.

[0493] Mitochondrial dysfunction leads to impaired calcium buffering, generation of free radicals that may participate in deleterious intracellular and extracellular processes, changes in mitochondrial permeability and oxidative damage which is observed in several neurodegenerative diseases. Neurodegenerative diseases linked to mitochondrial dysfunction include some forms of Alzheimer's disease, Friedreich's ataxia, familial amyotrophic lateral sclerosis, and Huntington's disease (Beal, M. F. (1998) Biochim. Biophys. Acta 1366:211-213). The myocardium is heavily dependent on oxidative metabolism, so mitochondrial dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol 13:190-197). Mitochondria are implicated in disorders of cell proliferation, since they play an important role in a cell's decision to proliferate or self-destruct through apoptosis. The oncoprotein Bc1-2, for example, promotes cell proliferation by stabilizing mitochondrial membranes so that apoptosis signals are not released (Susin, S. A. (1998) Biochim. Biophys. Acta 1366:151-165).

[0494] Transcription Factor Molecules

[0495] SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, transcription factor molecules.

[0496] Multicellular organisms are comprised of diverse cell types that differ dramatically both in structure and function. The identity of a cell is determined by its characteristic pattern of gene expression, and different cell types express overlapping but distinctive sets of genes throughout development. Spatial and temporal regulation of gene expression is critical for the control of cell proliferation, cell differentiation, apoptosis, and other processes that contribute to organismal development. Furthermore, gene expression is regulated in response to extracellular signals that mediate cell-cell communication and coordinate the activities of different cell types. Appropriate gene regulation also ensures that cells function efficiently by expressing only those genes whose functions are required at a given time.

[0497] Transcriptional regulatory proteins are essential for the control of gene expression. Some of these proteins function as transcription factors that initiate, activate, repress, or terminate gene transcription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements within or downstream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) Genes IV, Oxford University Press, New York N.Y., and Cell Press, Cambridge Mass., pp. 554-570.)

[0498] The double helix structure and repeated sequences of DNA create topological and chemical features which can be recognized by transcription factors. These features are hydrogen bond donor and acceptor groups, hydrophobic patches, major and minor grooves, and regular, repeated stretches of sequence which induce distinct bends in the helix. Typically, transcription factors recognize specific DNA sequence motifs of about 20 nucleotides in length. Multiple, adjacent transcription factor-binding motifs may be required for gene regulation.

[0499] Many transcription factors incorporate DNA-binding structural motifs which comprise either α helices or β sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.

[0500] The helix-turn-helix motif consists of two α helices connected at a fixed angle by a short chain of amino acids. One of the helices binds to the major groove. Helix-turn-helix motifs are exemplified by the homeobox motif which is present in homeodomain proteins. These proteins are critical for specifying the anterior-posterior body axis during development and are conserved throughout the animal kingdom. The Antennapedia and Ultrabithorax proteins of Drosophila melanogaster are prototypical homeodomain proteins (Pabo, C. O. and R. T. Sauer (1992) Annu. Rev. Biochem. 61:1053-1095).

[0501] The zinc finger motif, which binds zinc ions, generally contains tandem repeats of about 30 amino acids consisting of periodically spaced cysteine and histidine residues. Examples of this sequence pattern, designated C2H2 and C3HC4 (“RING” finger), have been described (Lewin, supra). Zinc finger proteins each contain an α helix and an antiparallel β sheet whose proximity and conformation are maintained by the zinc ion. Contact with DNA is made by the arginine prece ding the α helix and by the second, third, and sixth residues of the α helix. Variants of the zinc finger motif include poorly defined cysteine-rich motifs which bind zinc or other metal ions. These motifs may not contain histidine residues and are generally nonrepetitive.

[0502] The leucine zipper motif comprises a stretch of amino acids rich in leucine which can form an amphipathic α helix. This structure provides the basis for dimerization of two leucine zipper proteins. The region adjacent to the leucine zipper is usually basic, and upon protein dimerization, is optimally positioned for binding to the major groove. Proteins containing such motifs are generally referred to as bZIP transcription factors.

[0503] The helix-loop-helix motif (HLH) consists of a short ct helix connected by a loop to a longer α helix. The loop is flexible and allows the two helices to fold back against each other and to bind to DNA. The transcription factor Myc contains a prototypical HLH motif.

[0504] Most transcription factors contain characteristic DNA binding motifs, and variations on the above motifs and new motifs have been and are currently being characterized (Faisst, S. and S. Meyer (1992) Nucleic Acids Res. 20:3-26).

[0505] Many neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M. L. (1992) Cancer Surv. 15:89-104). Chromosomal translocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene transcription, potentially contributing to malignancy.

[0506] In addition, the immune system responds to infection or trauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, stroke, and infections (Isselbacher, K. J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).

[0507] Furthermore, the generation of multicellular organisms is based upon the induction and coordination of cell differentiation at the appropriate stages of development. Central to this process is differential gene expression, which confers the distinct identities of cells and tissues throughout the body. Failure to regulate gene expression during development can result in developmental disorders. Human developmental disorders caused by mutations in zinc finger-type transcriptional regulators include: urogenenital developmental abnormalities associated with WT1; Greig cephalopolysyndactyly, Pallister-Hall syndrome, and postaxial polydactyly type A (GLI3); and Townes-Brocks syndrome, characterized by anal, renal, limb, and ear abnormalities (SALL1) (Engelkamp, D. and V. van Heyningen (1996) Curr. Opin. Genet. Dev. 6:334-342; Kohlhase, J. et al. (1999) Am. J. Hum. Genet. 64:435-445).

[0508] Cell Membrane Molecules

[0509] SEQ ID NO:28 and SEQ ID NO:29 encode, for example, cell membrane molecules.

[0510] Eukaryotic cells are surrounded by plasma membranes which enclose the cell and maintain an environment inside the cell that is distinct from its surroundings. In addition, eukaryotic organisms are distinct from prokaryotes in possessing many intracellular organelle and vesicle structures. Many of the metabolic reactions which distinguish eukaryotic biochemistry from prokaryotic biochemistry take place within these structures. The plasma membrane and the membranes surrounding organelles and vesicles are composed of phosphoglycerides, fatty acids, cholesterol, phospholipids, glycolipids, proteoglycans, and proteins. These components confer identity and functionality to the membranes with which they associate.

[0511] Integral Membrane Proteins

[0512] The majority of known integral membrane proteins are transmembrane proteins (TM) which are characterized by an extracellular, a transmembrane, and an intracellular domain. TM domains are typically comprised of 15 to 25 hydrophobic amino acids which are predicted to adopt an α-helical conformation. TM proteins are classified as bitopic (Types I and II) and polytopic (Types III and IV) (Singer, S. J. (1990) Annu. Rev. Cell Biol. 6:247-296). Bitopic proteins span the membrane once while polytopic proteins contain multiple membrane-spanning segments. TM proteins function as cell-surface receptors, receptor-interacting proteins, transporters of ions or metabolites, ion channels, cell anchoring proteins, and cell type-specific surface antigens.

[0513] Many membrane proteins (MPs) contain amino acid sequence motifs that target these proteins to specific subcellular sites. Examples of these motifs include PDZ domains, KDEL, RGD, NGR, and GSL sequence motifs, von Willebrand factor A (vWFA) domains, and EGF-like domains. RGD, NGR, and GSL motif-containing peptides have been used as drug delivery agents in targeted cancer treatment of tumor vasculature (Arap, W. et al. (1998) Science 279:377-380). Furthermore, MPs may also contain amino acid sequence motifs, such as the carbohydrate recognition domain (CRD), that mediate interactions with extracellular or intracellular molecules.

[0514] G-Protein Coupled Receptors

[0515] G-protein coupled receptors (GPCR) are a superfamily of integral membrane proteins which transduce extracellular signals. GPCRs include receptors for biogenic amines, lipid mediators of inflammation, peptide hormones, and sensory signal mediators. The structure of these highly-conserved receptors consists of seven hydrophobic transmembrane regions, an extracellular N-terminus, and a cytoplasmic C-terminus. Three extracellular loops alternate with three intracellular loops to link the seven transmembrane regions. Cysteine disulfide bridges connect the second and third extracellular loops. The most conserved regions of GPCRs are the transmembrane regions and the first two cytoplasmic loops. A conserved, acidic-Arg-aromatic residue triplet present in the second cytoplasmic loop may interact with G proteins. A GPCR consensus pattern is characteristic of most proteins belonging to this superfamily (ExPASy PROSITE document PS00237; and Watson, S. and S. Arkinstall (1994) The G-protein Linked Receptor Facts Book, Academic Press, San Diego Calif., pp. 2-6). Mutations and changes in transcriptional activation of GPCR-encoding genes have been associated with neurological disorders such as schizophrenia, Parkinson's disease, Alzheimer's disease, drug addiction, and feeding disorders.

[0516] Scavenger Receptors

[0517] Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain. The extracellular domain contains a short spacer region, an α-helical coiled-coil region, and a triple helical collagen-like region. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phospholipids, and asbestos (Matsumoto, A. et al. (1990) Proc. Natl. Acad. Sci. USA 87:9133-9137; and Elomaa, O. et al. (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa.

[0518] Tetraspan Family Proteins

[0519] The transmembrane 4 superfamily (TM4SF) or tetraspan family is a multigene family encoding type III integral membrane proteins (Wright, M. D. and M. G. Tomlinson (1994) Immunol. Today 15:588-594). The TM4SF is comprised of membrane proteins which traverse the cell membrane four times. Members of the TM4SF include platelet and endothelial cell membrane proteins, melanoma-associated antigens, leukocyte surface glycoproteins, colonal carcinoma antigens, tumor-associated antigens, and surface proteins of the schistosome parasites (Jankowski, S. A. (1994) Oncogene 9:1205-1211). Members of the TM4SF share about 25-30% amino acid sequence identity with one another.

[0520] A number of TM4SF members have been implicated in signal transduction, control of cell adhesion, regulation of cell growth and proliferation, including development and oncogenesis, and cell motility, including tumor cell metastasis. Expression of TM4SF proteins is associated with a variety of tumors and the level of expression may be altered when cells are growing or activated.

[0521] Tumor Antigens

[0522] Tumor antigens are cell surface molecules that are differentially expressed in tumor cells relative to normal cells. Tumor antigens distinguish tumor cells immunologically from normal cells and provide diagnostic and therapeutic targets for human cancers (Takagi, S. et al. (1995) Int. J. Cancer 61:706-715; Liu, E. et al. (1992) Oncogene 7:1027-1032).

[0523] Leukocyte Antigens

[0524] Other types of cell surface antigens include those identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)-based “shot gun” techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into “clusters of differentiation” based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a “cluster of differentiation” or “CD” designation. Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques. CD antigens have been characterized as both transmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A. N. et al. (1995) The Leucocyte Antigen Facts Book, Academic Press, San Diego Calif., pp. 17-20.)

[0525] Ion Channels

[0526] Ion channels are found in the plasma membranes of virtually every cell in the body. For example, chloride channels mediate a variety of cellular functions including regulation of membrane potentials and absorption and secretion of ions across epithelial membranes. Chloride channels also regulate the pH of organelles such as the Golgi apparatus and endosomes (see, e.g., Greger, R. (1988) Annu. Rev. Physiol. 50:111-122). Electrophysiological and pharmacological properties of chloride channels, including ion conductance, current-voltage relationships, and sensitivity to modulators, suggest that different chloride channels exist in muscles, neurons, fibroblasts, epithelial cells, and lymphocytes.

[0527] Many ion channels have sites for phosphorylation by one or more protein kinases including protein kinase A, protein kinase C, tyrosine kinase, and casein kinase II, all of which regulate ion channel activity in cells. Inappropriate phosphorylation of proteins in cells has been linked to changes in cell cycle progression and cell differentiation. Changes in the cell cycle have been linked to induction of apoptosis or cancer. Changes in cell differentiation have been linked to diseases and disorders of the reproductive system, immune system, skeletal muscle, and other organ systems.

[0528] Proton Pumps

[0529] Proton ATPases comprise a large class of membrane proteins that use the energy of ATP hydrolysis to generate an electrochemical proton gradient across a membrane. The resultant gradient may be used to transport other ions across the membrane (Na⁺, K⁺, or Cl⁻) or to maintain organelle pH. Proton ATPases are further subdivided into the mitochondrial F-ATPases, the plasma membrane ATPases, and the vacuolar ATPases. The vacuolar ATPases establish and maintain an acidic pH within various organelles involved in the processes of endocytosis and exocytosis (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700).

[0530] Proton-coupled, 12 membrane-spanning domain transporters such as PEPT 1 and PEPT 2 are responsible for gastrointestinal absorption and for renal reabsorption of peptides using an electrochemical H⁺ gradient as the driving force. Another type of peptide transporter, the TAP transporter, is a heterodimer consisting of TAP 1 and TAP 2 and is associated with antigen processing. Peptide antigens are transported across the membrane of the endoplasmic reticulum by TAP so they can be expressed on the cell surface in association with MHC molecules. Each TAP protein consists of multiple hydrophobic membrane spanning segments and a highly conserved ATP-binding cassette (Boll, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:284-289). Pathogenic microorganisms, such as herpes simplex virus, may encode inhibitors of TAP-mediated peptide transport in order to evade immune surveillance (Marusina, K. and J. J Manaco (1996) Curr. Opin. Hematol. 3:19-26).

[0531] ABC Transporters

[0532] The ATP-binding cassette (ABC) transporters, also called the “traffic ATPases”, comprise a superfamily of membrane proteins that mediate transport and channel functions in prokaryotes and eukaryotes (Higgins, C. F. (1992) Annu. Rev. Cell Biol. 8:67-113). ABC proteins share a similar overall structure and significant sequence homology. All ABC proteins contain a conserved domain of approximately two hundred amino acid residues which includes one or more nucleotide binding domains. Mutations in ABC transporter genes are associated with various disorders, such as hyperbilirubinemia II/Dubin-Johnson syndrome, recessive Stargardt's disease, X-linked adrenoleukodystrophy, multidrug resistance, celiac disease, and cystic fibrosis.

[0533] Peripheral and Anchored Membrane Proteins

[0534] Some membrane proteins are not membrane-spanning but are attached to the plasma membrane via membrane anchors or interactions with integral membrane proteins. Membrane anchors are covalently joined to a protein post-translationally and include such moieties as prenyl, myristyl, and glycosylphosphatidyl inositol groups. Membrane localization of peripheral and anchored proteins is important for their function in processes such as receptor-mediated signal transduction. For example, prenylation of Ras is required for its localization to the plasma membrane and for its normal and oncogenic functions in signal transduction.

[0535] Vesicle Coat Proteins

[0536] Intercellular communication is essential for the development and survival of multicellular organisms. Cells communicate with one another through the secretion and uptake of protein signaling molecules. The uptake of proteins into the cell is achieved by the endocytic pathway, in which the interaction of extracellular signaling molecules with plasma membrane receptors results in the formation of plasma membrane-derived vesicles that enclose and transport the molecules into the cytosol. These transport vesicles fuse with and mature into endosomal and lysosomal (digestive) compartments. The secretion of proteins from the cell is achieved by exocytosis, in which molecules inside of the cell proceed through the secretory pathway. In this pathway, molecules transit from the ER to the Golgi apparatus and finally to the plasma membrane, where they are secreted from the cell.

[0537] Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. Vesicle formation occurs when a region of membrane buds off from the donor organelle. The membrane-bound vesicle contains proteins to be transported and is surrounded by a proteinaceous coat, the components of which are recruited from the cytosol. Two different classes of coat protein have been identified. Clathrin coats form on vesicles derived from the TGN and PM, whereas coatomer (COP) coats form on vesicles derived from the ER and Golgi. COP coats can be further classified as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the ER to the Golgi (Mellman, supra).

[0538] In clathrin-based vesicle formation, adapter proteins bring vesicle cargo and coat proteins together at the surface of the budding membrane. Adapter protein-1 and -2 select cargo from the TGN and plasma membrane, respectively, based on molecular information encoded on the cytoplasmic tail of integral membrane cargo proteins. Adapter proteins also recruit clathrin to the bud site. Clathrin is a protein complex consisting of three large and three small polypeptide chains arranged in a three-legged structure called a triskelion. Multiple triskelions and other coat proteins appear to self-assemble on the membrane to form a coated pit. This assembly process may serve to deform the membrane into a budding vesicle. GTP-bound ADP-ribosylation factor (Arf) is also incorporated into the coated assembly. Another small G-protein, dynamin, forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to seal the bud, thereby releasing the vesicle. The coated vesicle complex is then transported through the cytosol. During the transport process, Arf-bound GTP is hydrolyzed to GDP, and the coat dissociates from the transport vesicle (West, M. A. et al. (1997) J. Cell Biol. 138:1239-1254).

[0539] Vesicles which bud from the ER and the Golgi are covered with a protein coat similar to the clathrin coat of endocytic and TGN vesicles. The coat protein (COP) is assembled from cytosolic precursor molecules at specific budding regions on the organelle. The COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta′-, gamma-, delta-, epsilon- and zeta-COP. The coatomer complex binds to dilysine motifs contained on the cytoplasmic tails of integral membrane proteins. These include the KKXX retrieval motif of membrane proteins of the ER and dibasic/diphenylamine motifs of members of the p24 family. The p24 family of type I membrane proteins represent the major membrane proteins of COPI vesicles (Harter, C. and F. T. Wieland (1998) Proc. Natl. Acad. Sci. USA 95:11649-11654).

[0540] Organelle Associated Molecules

[0541] SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules.

[0542] Eukaryotic cells are organized into various cellular organelles which has the effect of separating specific molecules and their functions from one another and from the cytosol. Within the cell, various membrane structures surround and define these organelles while allowing them to interact with one another and the cell environment through both active and passive transport processes.

[0543] Important cell organelles include the nucleus, the Golgi apparatus, the endoplasmic reticulum, mitochondria, peroxisomes, lysosomes, endosomes, and secretory vesicles.

[0544] Nucleus

[0545] The cell nucleus contains all of the genetic information of the cell in the form of DNA, and the components and machinery necessary for replication of DNA and for transcription of DNA into RNA. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Inc., New York N.Y., pp. 335-399.) DNA is organized into compact structures in the nucleus by interactions with various DNA-binding proteins such as histones and non-histone chromosomal proteins. DNA-specific nucleases, DNAses, partially degrade these compacted structures prior to DNA replication or transcription. DNA replication takes place with the aid of DNA helicases which unwind the double-stranded DNA helix, and DNA polymerases that duplicate the separated DNA strands.

[0546] Transcriptional regulatory proteins are essential for the control of gene expression. Some of these proteins function as transcription factors that initiate, activate, repress, or terminate gene transcription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements within or downstream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) Genes IV, Oxford University Press, New York N.Y., and Cell Press, Cambridge Mass., pp. 554-570.) Many transcription factors incorporate DNA-binding structural motifs which comprise either α helices or β sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.

[0547] Many neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M. L. (1992) Cancer Surv. 15:89-104). Chromosomal translocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene transcription, potentially contributing to malignancy.

[0548] In addition, the immune system responds to infection or trauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, stroke, and infections (Isselbacher, K. J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).

[0549] Transcription of DNA into RNA also takes place in the nucleus catalyzed by RNA polymerases. Three types of RNA polymerase exist. RNA polymerase I makes large ribosomal RNAs, while RNA polymerase III makes a variety of small, stable RNAs including 5S ribosomal RNA and the transfer RNAs (tRNA). RNA polymerase II transcribes genes that will be translated into proteins. The primary transcript of RNA polymerase II is called heterogenous nuclear RNA (hnRNA), and must be further processed by splicing to remove non-coding sequences called introns. RNA splicing is mediated by small nuclear ribonucleoprotein complexes, or snRNPs, producing mature messenger RNA (mRNA) which is then transported out of the nucleus for translation into proteins.

[0550] Nucleolus

[0551] The nucleolus is a highly organized subcompartment in the nucleus that contains high concentrations of RNA and proteins and functions mainly in ribosomal RNA synthesis and assembly (Alberts, et al. supra, pp. 379-382). Ribosomal RNA (rRNA) is a structural RNA that is complexed with proteins to form ribonucleoprotein structures called ribosomes. Ribosomes provide the platform on which protein synthesis takes place.

[0552] Ribosomes are assembled in the nucleolus initially from a large, 45S rRNA combined with a variety of proteins imported from the cytoplasm, as well as smaller, 5S rRNAs. Later processing of the immature ribosome results in formation of smaller ribosomal subunits which are transported from the nucleolus to the cytoplasm where they are assembled into functional ribosomes.

[0553] Endoplasmic Reticulum

[0554] In eukaryotes, proteins are synthesized within the endoplasmic reticulum (ER), delivered from the ER to the Golgi apparatus for post-translational processing and sorting, and transported from the Golgi to specific intracellular and extracellular destinations. Synthesis of integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on the rough endoplasmic reticulum (ER). The rough ER is so named because of the rough appearance in electron micrographs imparted by the attached ribosomes on which protein synthesis proceeds. Synthesis of proteins destined for the ER actually begins in the cytosol with the synthesis of a specific signal peptide which directs the growing polypeptide and its attached ribosome to the ER membrane where the signal peptide is removed and protein synthesis is completed. Soluble proteins destined for the ER lumen, for secretion, or for transport to the lumen of other organelles pass completely into the ER lumen. Transmembrane proteins destined for the ER or for other cell membranes are translocated across the ER membrane but remain anchored in the lipid bilayer of the membrane by one or more membrane-spanning α-helical regions.

[0555] Translocated polypeptide chains destined for other organelles or for secretion also fold and assemble in the ER lumen with the aid of certain “resident” ER proteins. Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form intramolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imide bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R. E. et al. (1984) Science 226:544-547). Molecular “chaperones” such as BiP (binding protein) in the ER recognize incorrectly folded proteins as well as proteins not yet folded into their final form and bind to them, both to prevent improper aggregation between them, and to promote proper folding.

[0556] The “N-linked” glycosylation of most soluble secreted and membrane-bound proteins by oligosacchrides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase.

[0557] Golgi Apparatus

[0558] The Golgi apparatus is a complex structure that lies adjacent to the ER in eukaryotic cells and serves primarily as a sorting and dispatching station for products of the ER (Alberts, et al. supra, pp. 600-610). Additional posttranslational processing, principally additional glycosylation, also occurs in the Golgi. Indeed, the Golgi is a major site of carbohydrate synthesis, including most of the glycosaminoglycans of the extracellular matrix. N-linked oligosaccharides, added to proteins in the ER, are also further modified in the Golgi by the addition of more sugar residues to form complex N-linked oligosaccharides. “O-linked” glycosylation of proteins also occurs in the Golgi by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalyzed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W. H. Freeman and Co., New York N.Y., pp.700-708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface.

[0559] The terminal compartment of the Golgi is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport (or secretory) vesicles destined for intracellular compartments, such as lysosomes, bud off of the TGN. Other transport vesicles bud off containing proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurotransmitters, and digestive enzymes.

[0560] Vacuoles

[0561] The vacuole system is a collection of membrane bound compartments in eukaryotic cells that functions in the processes of endocytosis and exocytosis. They include phagosomes, lysosomes, endosomes, and secretory vesicles. Endocytosis is the process in cells of internalizing nutrients, solutes or small particles (pinocytosis) or large particles such as internalized receptors, viruses, bacteria, or bacterial toxins (phagocytosis). Exocytosis is the process of transporting molecules to the cell surface. It facilitates placement or localization of membrane-bound receptors or other membrane proteins and secretion of hormones, neurotransmitters, digestive enzymes, wastes, etc.

[0562] A common property of all of these vacuoles is an acidic pH environment ranging from approximately pH 4.5-5.0. This acidity is maintained by the presence of a proton ATPase that uses the energy of ATP hydrolysis to generate an electrochemical proton gradient across a membrane (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700). Eukaryotic vacuolar proton ATPase (vp-ATPase) is a multimeric enzyme composed of 3-10 different subunits. One of these subunits is a highly hydrophobic polypeptide of approximately 16 kDa that is similar to the proteolipid component of vp-ATPases from eubacteria, fungi, and plant vacuoles (Mandel, M. et al. (1988) Proc. Natl. Acad. Sci. USA 85:5521-5524). The 16 kDa proteolipid component is the major subunit of the membrane portion of vp-ATPase and functions in the transport of protons across the membrane.

[0563] Lysosomes

[0564] Lysosomes are membranous vesicles containing various hydrolytic enzymes used for the controlled intracellular digestion of macromolecules. Lysosomes contain some 40 types of enzymes including proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, and sulfatases, all of which are acid hydrolases that function at a pH of about 5. Lysosomes are surrounded by a unique membrane containing transport proteins that allow the final products of macromolecule degradation, such as sugars, amino acids, and nucleotides, to be transported to the cytosol where they may be either excreted or reutilized by the cell. A vp-ATPase, such as that described above, maintains the acidic environment necessary for hydrolytic activity (Alberts, supra, pp. 610-611).

[0565] Endosomes

[0566] Endosomes are another type of acidic vacuole that is used to transport substances from the cell surface to the interior of the cell in the process of endocytosis. Like lysosomes, endosomes have an acidic environment provided by a vp-ATPase (Alberts et al. supra, pp. 610-618). Two types of endosomes are apparent based on tracer uptake studies that distinguish their time of formation in the cell and their cellular location. Early endosomes are found near the plasma membrane and appear to function primarily in the recycling of internalized receptors back to the cell surface. Late endosomes appear later in the endocytic process close to the Golgi apparatus and the nucleus, and appear to be associated with delivery of endocytosed material to lysosomes or to the TGN where they may be recycled. Specific proteins are associated with particular transport vesicles and their target compartments that may provide selectivity in targeting vesicles to their proper compartments. A cytosolic prenylated GTP-binding protein, Rab, is one such protein. Rabs 4, 5, and 11 are associated with the early endosome, whereas Rabs 7 and 9 associate with the late endosome.

[0567] Mitochondria

[0568] Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of transport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells.

[0569] Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted to pyruvate in the cytoplasm. Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to CO₂ coupled by enzymes to the transport of electrons from NADH and FADH₂ to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P_(i).

[0570] Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to CO₂ with concomitant formation of NADH, FADH₂, and GTP. In oxidative phosphorylation, the transfer of electrons from NADH and FADH₂ to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P_(i) by the F₀F₁ ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F₀F₁ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c₁, FeS protein, and cytochrome c oxidase.

[0571] Peroxisomes

[0572] Peroxisomes, like mitochondria, are a major site of oxygen utilization. They contain one or more enzymes, such as catalase and urate oxidase, that use molecular oxygen to remove hydrogen atoms from specific organic substrates in an oxidative reaction that produces hydrogen peroxide (Alberts, supra, pp. 574-577). Catalase oxidizes a variety of substrates including phenols, formic acid, formaldehyde, and alcohol and is important in peroxisomes of liver and kidney cells for detoxifying various toxic molecules that enter the bloodstream. Another major function of oxidative reactions in peroxisomes is the breakdown of fatty acids in a process called β oxidation. β oxidation results in shortening of the alkyl chain of fatty acids by blocks of two carbon atoms that are converted to acetyl CoA and exported to the cytosol for reuse in biosynthetic reactions.

[0573] Also like mitochondria, peroxisomes import their proteins from the cytosol using a specific signal sequence located near the C-terminus of the protein. The importance of this import process is evident in the inherited human disease Zellweger syndrome, in which a defect in importing proteins into perixosomes leads to a perixosomal deficiency resulting in severe abnormalities in the brain, liver, and kidneys, and death soon after birth. One form of this disease has been shown to be due to a mutation in the gene encoding a perixosomal integral membrane protein called peroxisome assembly factor-1.

[0574] The discovery of new human molecules for diagnostics and therapeutics satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with human molecules.

SUMMARY OF THE INVENTION

[0575] The present invention relates to nucleic acid sequences comprising human diagnostic and therapeutic polynucleotides (dithp) as presented in the Sequence Listing. Some of the dithp uniquely identify genes encoding human structural, functional, and regulatory molecules.

[0576] The invention provides an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52. In another alternative, the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The invention further provides a composition for the detection of expression of human diagnostic and therapeutic polynucleotides, comprising at least one isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d); and a detectable label.

[0577] The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof. In one alternative, the probe comprises at least 30 contiguous nucleotides. In another alternative, the probe comprises at least 60 contiguous nucleotides.

[0578] The invention further provides a recombinant polynucleotide comprising a promoter sequence operably linked to an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide. In a further alternative, the invention provides a method for producing a human diagnostic and therapeutic polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the human diagnostic and therapeutic polypeptide, wherein said cell is transformed with the recombinant polynucleotide, and b) recovering the human diagnostic and therapeutic polypeptide so expressed.

[0579] The invention also provides a purified human diagnostic and therapeutic polypeptide (DITHP) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52. Additionally, the invention provides an isolated antibody which specifically binds to the human diagnostic and therapeutic polypeptide. The invention further provides a method of identifying a test compound which specifically binds to the human diagnostic and therapeutic polypeptide, the method comprising the steps of a) providing a test compound; b) combining the human diagnostic and therapeutic polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the human diagnostic and therapeutic polypeptide to the test compound, thereby identifying the test compound which specifically binds the human diagnostic and therapeutic polypeptide.

[0580] The invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide seque.nce'selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The invention also provides a method for generating a transcript image of a sample which contains polynucleotides. The method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.

[0581] Additionally, the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.

[0582] The invention further provides a method for detecting a target polynucleotide in a sample for toxicity testing of a compound, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof, and c) comparing the presence, absence or amount of said target polynucleotide in a first biological sample and a second biological sample, wherein said first biological sample has been contacted with said compound, and said second sample is a control, whereby a change in presence, absence or amount of said target polynucleotide in said first sample, as compared with said second sample, is indicative of toxic response to said compound.

DESCRIPTION OF THE TABLES

[0583] Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with their GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.

[0584] Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions. The reading frames of the polynucleotide segments and the Pfam hits, Pfam descriptions, and E-values corresponding to the polypeptide domains encoded by the polynucleotide segments are indicated.

[0585] Table 3 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions. The reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated.

[0586] Table 4 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component IDs) corresponding to each template. The component sequences, which were used to assemble the template sequences, are defined by the indicated “start” and “stop” nucleotide positions along each template.

[0587] Table 5 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention. The first column of Table 5 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).

[0588] Detailed Description of the Invention

[0589] Before the nucleic acid sequences and methods are presented, it is to be understood that this invention is not limited to the particular machines, methods, and materials described. Although particular embodiments are described, machines, methods, and materials similar or equivalent to these embodiments may be used to practice the invention. The preferred machines, methods, and materials set forth are not intended to limit the scope of the invention which is limited only by the appended claims.

[0590] The singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. All technical and scientific terms have the meanings commonly understood by one of ordinary skill in the art. All publications are incorporated by reference for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are presented and which might be used in connection with the invention. Nothing in the specification is to be construed as an admission that the invention is not entitled to antedate such disclosure by-virtue of prior invention.

[0591] Definitions

[0592] As used herein, the lower case “dithp” refers to a nucleic acid sequence, while the upper case “DITHP” refers to an amino acid sequence encoded by dithp. A “full-length” dithp refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.

[0593] “Adjuvants” are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which may be administered to increase a host's immunological response.

[0594] “Allele” refers to an alternative form of a nucleic acid sequence. Alleles result from a “mutation,” a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence. The present invention encompasses allelic dithp.

[0595] “Amino acid sequence” refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.

[0596] “Amplification” refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.

[0597] “Antibody” refers to intact molecules as well as to fragments thereof, such as Fab, F(ab′)₂, and Fv fragments, which are capable of binding the epitopic determinant. Antibodies that bind DITHP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

[0598] “Antisense sequence” refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2′-methoxyethyl sugars or 2′-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2′-deoxyuracil, or 7-deaza-2′-deoxyguanosine.

[0599] “Antisense sequence” refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.

[0600] “Antisense technology” refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.

[0601] A “bin” is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.

[0602] “Biologically active” refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.

[0603] “Clone joining” is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants.

[0604] “Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5′-A-G-T-3′ pairs with its complement 3′-T-C-A-5′).

[0605] A “component sequence” is a nucleic acid sequence selected by a computer program such as PHRED and used to assemble a consensus or template sequence from one or more component sequences.

[0606] A “consensus sequence” or “template sequence” is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GELVIEW fragment assembly system (Genetics Computer Group (GCG), Madison Wis.) or using a relational database management system (RDMS).

[0607] “Conservative amino acid substitutions” are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions. Original Residue Conservative Substitution Ala Gly, Ser Arg His, Lys Asn Asp, Gln, His Asp Asn, Glu Cys Ala, Ser Gln Asn, Glu, His Glu Asp, Gln, His Gly Ala His Asn, Arg, Gln, Glu Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe, Tyr Tyr His, Phe, Trp Val Ile, Leu, Thr

[0608] Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.

[0609] “Deletion” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent.

[0610] “Derivative” refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.

[0611] “E-value” refers to the statistical probability that a match between two sequences occurred by chance.

[0612] A “fragment” is a unique portion of dithp or DITHP which is identical in sequence to but shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the figures, may be encompassed by the present embodiments.

[0613] A fragment of dithp comprises a region of unique polynucleotide sequence that specifically identifies dithp, for example, as distinct from any other sequence in the same genome. A fragment of dithp is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish dithp from related polynucleotide sequences. The precise length of a fragment of dithp and the region of dithp to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0614] A fragment of DITHP is encoded by a fragment of dithp. A fragment of DITHP comprises a region of unique amino acid sequence that specifically identifies DITHP. For example, a fragment of DITHP is useful as an immunogenic peptide for the development of antibodies that specifically recognize DITHP. The precise length of a fragment of DITHP and the region of DITHP to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0615] A “full length” nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a “full length” polypeptide.

[0616] “Hit” refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E-value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value.

[0617] “Homology” refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of a dithp or between a reference amino acid sequence and a fragment of a DITHP.

[0618] “Hybridization” refers to the process by which a strand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the “washing” step. The defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.

[0619] Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5° C. to 20° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating T_(m) and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; specifically see volume 2, chapter 9.

[0620] High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68° C. in the presence of about 0.2×SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65° C., 60° C., or 55° C. may be used. SSC concentration may be varied from about 0.2 to 2×SSC, with SDS being present at about 0.1%. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 μg/ml. Useful variations on these conditions will be readily apparent to those skilled in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.

[0621] Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.

[0622] “Immunogenic” describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.

[0623] “Insertion” or “addition” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.

[0624] “Labeling” refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.

[0625] “Microarray” is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate. The substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.

[0626] The terms “element” and “array element” refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.

[0627] “Linkers” are short stretches of nucleotide sequence which may be added to a vector or a dithp to create restriction endonuclease sites to facilitate cloning. “Polylinkers” are engineered to incorporate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5′ or 3′ overhangs (e.g., BamHI, EcoRI, and HindIII) and those which provide blunt ends (e.g., EcoRV, SnaBI, and StuI).

[0628] “Naturally occurring” refers to an endogenous polynucleotide or polypeptide that may be isolated from viruses or prokaryotic or eukaryotic cells.

[0629] “Nucleic acid sequence” refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, oligonucleotide, or polynucleotide. The nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense (complementary) strand.

[0630] “Oligomer” refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and 30 nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used as, e.g., primers for PCR, and are usually chemically synthesized.

[0631] “Operably linked” refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.

[0632] “Peptide nucleic acid” (PNA) refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.

[0633] The phrases “percent identity” and “% identity”, as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.

[0634] Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison Wis.). CLUSTAL V is described in Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153 and in Higgins, D. G. et al. (1992) CABIOS 8:189-191. For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and “diagonals saved”=4. The “weighted” residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polynucleotide sequence pairs.

[0635] Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, Md., and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including “blastn,” that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases. Also available is a tool called “BLAST 2 Sequences” that is used for direct pairwise comparison of two nucleotide sequences. “BLAST 2 Sequences” can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/b12/. The “BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such default parameters may be, for example:

[0636] Matrix: BLOSUM62

[0637] Reward for match: 1

[0638] Penalty for mismatch: −2

[0639] Open Gap: 5 and Extension Gap: 2 penalties

[0640] Gap x drop-off: 50

[0641] Expect: 10

[0642] Word Size: 11

[0643] Filter: on

[0644] Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.

[0645] Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.

[0646] The phrases “percent identity” and “% identity”, as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide.

[0647] Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=1, gap penalty=3, window=5, and “diagonals saved”=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polypeptide sequence pairs.

[0648] Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) with blastp set at default parameters. Such default parameters may be, for example:

[0649] Matrix: BLOSUM62

[0650] Open Gap: 11 and Extension Gap: 1 penalty

[0651] Gap x drop-off: 50

[0652] Expect: 10

[0653] Word Size: 3

[0654] Filter: on

[0655] Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.

[0656] “Post-translational modification” of a DITHP may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the DITHP.

[0657] “Probe” refers to dithp or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. “Primers” are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).

[0658] Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing, may be used.

[0659] Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; Ausubel et al., 1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences, New York N.Y.; Innis et al., 1990, PCR Protocols, A Guide to Methods and Applications, Academic Press, San Diego Calif. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge Mass.).

[0660] Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas Tex.) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge Mass.) allows the user to input a “mispriming library,” in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.

[0661] “Purified” refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.

[0662] A “recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence.

[0663] Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.

[0664] Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

[0665] “Regulatory element” refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3′ untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.

[0666] “Reporter” molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

[0667] An “RNA equivalent,” in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

[0668] “Sample”,is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots or imprints from such cells or tissues).

[0669] “Specific binding” or “specifically binding” refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope “A,” the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.

[0670] “Substitution” refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.

[0671] “Substrate” refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.

[0672] A “transcript image” refers to the collective pattern of gene expression by a particular tissue or cell type under given conditions at a given time.

[0673] “Transformation” refers to a process by which exogenous DNA enters a recipient cell. Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.

[0674] “Transformants” include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.

[0675] A “transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.

[0676] A “variant” of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 30%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or even at least 98% greater sequence identity over a certain defined length. The variant may result in “conservative” amino acid changes which do not affect structural and/or chemical properties. A variant may be described as, for example, an “allelic” (as defined above), “splice,” “species,” or “polymorphic” variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymorphic variants also may encompass “single nucleotide polymorphisms” (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

[0677] In an alternative, variants of the polynucleotides of the present invention may be generated through recombinant methods. One possible method is a DNA shuffling technique such as MOLECULARBREEDING (Maxygen Inc., Santa Clara Calif.; described in U.S. Pat. No. 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F. C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of DITHP, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through “artificial” breeding and rapid molecular evolution. For example, fragments of a single; gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.

[0678] A “variant” of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% or greater sequence identity over a certain defined length of one of the polypeptides.

[0679] The Invention

[0680] In a particular embodiment, cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into “consensus” or “template” sequences which are designated by the template identification numbers (template IDs) in column 2 of Table 1. The sequence identification numbers (SEQ ID NO:s) corresponding to the template IDs are shown in column 1. The template sequences have similarity to GenBank sequences, or “hits,” as designated by the GI Numbers in column 3. The statistical probability of each GenBank hit is indicated by a probability score in column 4, and the functional annotation corresponding to each GenBank hit is listed in column 5.

[0681] The invention incorporates the nucleic acid sequences of these templates as disclosed in the Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in human molecules. The invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments. In this manner, the sequences of the present invention are used to develop a transcript image for a particular cell or tissue.

[0682] Derivation of Nucleic Acid Sequences

[0683] cDNA was isolated from libraries constructed using RNA derived from normal and diseased human tissues and cell lines. The human tissues and cell lines used for cDNA library construction were selected from a broad range of sources to provide a diverse population of cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA library construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto Calif.). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.

[0684] Cell lines used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheliomas, cervical carcinoma, lung fibroblasts, and endothelial cells. Such cell lines include, for example, THP-1, Jurkat, HUVEC, hNT2, WI38, HeLa, and other cell lines commonly used and available from public depositories (American Type Culture Collection, Manassas Va.). Prior to mRNA isolation, cell lines were untreated, treated with a pharmaceutical agent such as 5′-aza-2′-deoxycytidine, treated with an activating agent such as lipopolysaccharide in the case of leukocytic cell lines, or, in the case of endothelial cell lines, subjected to shear stress.

[0685] Sequencing of the cDNAs

[0686] Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase 1SEQUENASE DNA polymerase (U.S. Biochemical Corporation, Cleveland Ohio), Taq polymerase (PE Biosystems, Foster City Calif.), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc. (Amersham Pharmacia Biotech), Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies Inc. (Life Technologies), Gaithersburg Md.), to extend the nucleic acid sequence from an oligonucleotide primer annealed to the DNA template of interest. Methods have been developed for the use of both single-stranded and double-stranded templates. Chain termination reaction products may be electrophoresed on urea-polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides). Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed. Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno Nev.), Peltier thermal cycler (PTC200; MJ Research, Inc. (MJ Research), Watertown Mass.), and ABI CATALYST 800 thermal cycler (PE Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (PE Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale Calif.) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.

[0687] The nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the-art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art. Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F. M. et al. (1997) Short Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.; and Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y.)

[0688] Assembly of cDNA Sequences

[0689] Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GELVIEW fragment assembly system (GCG), or other methods known in the art.

[0690] Alternatively, cDNA sequences are used as “component” sequences that are assembled into “template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quality scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, Calif.).

[0691] A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by “n's”, or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed. The processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available. When additional sequences are added into the RDMS, a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves. After the new sequences have been assigned to templates, the templates can be merged into bins. If multiple templates exist in one bin, the bin can be split and the templates reannotated.

[0692] Once gene bins have been generated based upon sequence alignments, bins are “clone joined” based upon clone information. Clone joining occurs when the 5′ sequence of one clone is present in one bin and the 3′ sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged.

[0693] A resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length. With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete “second strand” synthesis. Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene.

[0694] Analysis of the cDNA Sequences

[0695] The cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra, Chapter 7.7; Meyers, R. A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp. 856-853; and Table 5.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J. W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.

[0696] Computer programs known to those of skill in the art for performing computer-assisted searches for amino acid and nucleic acid sequence similarity, include, for example, Basic Local Alignment Search Tool (BLAST; Altschul, S. F. (1993) J. Mol. Evol. 36:290-300; Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410). BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (Karlin, S. et al. (1988) Proc. Natl. Acad. Sci. USA 85:841-845). Using an appropriate search tool (e.g., BLAST or HMM), GenBank, SwissProt, BLOCKS, PFAM and other databases may be searched for sequences containing regions of homology to a query dithp or DITHP of the present invention.

[0697] Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in “Relational Database for Storing Biomolecule Information,” U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; “Project-Based Full-Length Biomolecular Sequence Database,” U.S. Ser. No. 08/811,758, filed Mar. 6, 1997; and “Relational Database and System for Storing Information Relating to Biomolecular Sequences,” U.S. Ser. No. 09/034,807, filed Mar. 4, 1998, all of which are incorporated by reference herein in their entirety.

[0698] Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in “Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data,” U.S. Ser. No. 08/812,290, filed Mar. 6, 1997, incorporated herein by reference.

[0699] Identification of Human Diagnostic and Therapeutic Molecules Encoded by dithp

[0700] The identities of the DITHP encoded by the dithp of the present invention were obtained by analysis of the assembled cDNA sequences. SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5 encode, for example, human enzyme molecules. SEQ ID NO:6 and SEQ ID NO:7 encode, for example, receptor molecules. SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12 encode, for example, intracellular signaling molecules. SEQ ID NO:13 encodes, for example, a membrane transport molecule. SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:20 encode, for example, nucleic acid synthesis and modification molecules. SEQ ID NO:21 and SEQ ID NO:22 encode, for example, adhesion molecules. SEQ ID NO:23 and SEQ ID NO:24 encode, for example, electron transfer associated molecules. SEQ ID NO:25 encodes, for example, a secreted/extracellular matrix molecule. SEQ ID NO:26 and SEQ ID NO:27 encode, for example, cytoskeletal molecules. SEQ ID NO:28 and SEQ ID NO:29 encode, for example, cell membrane molecules. SEQ ID NO:30 and SEQ ID NO:31 encode, for example, ribosomal molecules. SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, transcription factor molecules. SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules. SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, and SEQ ID NO:50 encode, for example, biochemical pathway molecules. SEQ ID NO:51 and SEQ ID NO:52 encode, for example, molecules associated with growth and development.

[0701] Sequences of Human Diagnostic and Therapeutic Molecules

[0702] The dithp of the present invention may be used for a variety of diagnostic and therapeutic purposes. For example, a dithp may be used to diagnose a particular condition, disease, or disorder associated with human molecules. Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder, such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an autoimmune/inflammatory disorder, such as inflammation, actinic keratosis, acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis, cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmal nocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowel syndrome, episodic lymphopenia with lymphocytotoxins, mixed connective tissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, myelofibrosis, osteoarthritis, osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, primary thrombocythemia, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, trauma, and hematopoietic cancer including lymphoma, leukemia, and myeloma; an infection caused by a viral agent classified as adenovirus, arenavirus, bunyavirus, calicivirus, coronavirus, filovirus, hepadnavirus, herpesvirus, flavivirus, orthomyxovirus, parvovirus, papovavirus, paramyxovirus, picornavirus, poxvirus, reovirus, retrovirus, rhabdovirus, or togavirus; an infection caused by a bacterial agent classified as pneumococcus, staphylococcus, streptococcus, bacillus, corynebacterium, clostridium, meningococcus, gonococcus, listeria, moraxella, kingella, haemophilus, legionella, bordetella, gram-negative enterobacterium including shigella, salmonella, or campylobacter, pseudomonas, vibrio, brucella, francisella, yersinia, bartonella, norcardium, actinomyces, mycobacterium, spirochaetale, rickettsia, chlamydia, or mycoplasma; an infection caused by a fungal agent classified as aspergillus, blastomyces, dermatophytes, cryptococcus, coccidioides, malasezzia, histoplasma, or other mycosis-causing fungal agent; and an infection caused by a parasite classified as plasmodium or malaria-causing, parasitic entamoeba, leishmania, trypanosoma, toxoplasma, pneumocystis carinii, intestinal protozoa such as giardia, trichomonas, tissue nematode such as trichinella, intestinal nematode such as ascaris, lymphatic filarial nematode, trematode such as schistosoma, and cestrode such as tapeworm; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; an endocrine disorder such as a disorder of the hypothalamus and/or pituitary resulting from lesions such as a primary brain tumor, adenoma, infarction associated with pregnancy, hypophysectomy, aneurysm, vascular malformation, thrombosis, infection, immunological disorder, and complication due to head trauma; a disorder associated with hypopituitarism including hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism; a disorder associated with hyperpituitarism including acromegaly, giantism, and syndrome of inappropriate antidiuretic hormone (ADH) secretion (SIADH) often caused by benign adenoma; a disorder associated with hypothyroidism including goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism; a disorder associated with hyperthyroidism including thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease; a disorder associated with hyperparathyroidism including Conn disease (chronic hypercalemia); a pancreatic disorder such as Type I or Type II diabetes mellitus and associated complications; a disorder associated with the adrenals such as hyperplasia, carcinoma, or adenoma of the adrenal cortex, hypertension associated with alkalosis, amyloidosis, hypokalemia, Cushing's disease, Liddle's syndrome, and Arnold-Healy-Gordon syndrome, pheochromocytoma tumors, and Addison's disease; a disorder associated with gonadal steroid hormones such as: in women, abnormal prolactin production, infertility, endometriosis, perturbation of the menstrual cycle, polycystic ovarian disease, hyperprolactinemia, isolated gonadotropin deficiency, amenorrhea, galactorrhea, hermaphroditism, hirsutism and virilization, breast cancer, and, in post-menopausal women, osteoporosis; and, in men, Leydig cell deficiency, male climacteric phase, and germinal cell aplasia, a hypergonadal disorder associated with Leydig cell tumors, androgen resistance associated with absence of androgen receptors, syndrome of 5 α-reductase, and gynecomastia; a metabolic disorder such as Addison's disease, cerebrotendinous xanthomatosis, congenital adrenal hyperplasia, coumarin resistance, cystic fibrosis, diabetes, fatty hepatocirrhosis, fructose-1,6-diphosphatase deficiency, galactosemia, goiter, glucagonoma, glycogen storage diseases, hereditary fructose intolerance, hyperadrenalism, hypoadrenalism, hyperparathyroidism, hypoparathyroidism, hypercholesterolemia, hyperthyroidism, hypoglycemia, hypothyroidism, hyperlipidemia, hyperlipemia, lipid myopathies, lipodystrophies, lysosomal storage diseases, mannosidosis, neuraminidase deficiency, obesity, pentosuria phenylketonuria, pseudovitamin D-deficiency rickets; disorders of carbohydrate metabolism such as congenital type II dyserythropoietic anemia, diabetes, insulin-dependent diabetes mellitus, non-insulin-dependent diabetes mellitus, fructose-1,6-diphosphatase deficiency, galactosemia, glucagonoma, hereditary fructose intolerance, hypoglycemia, mannosidosis, neuraminidase deficiency, obesity, galactose epimerase deficiency, glycogen storage diseases, lysosomal storage diseases, fructosuria, pentosuria, and inherited abnormalities of pyruvate metabolism; disorders of lipid metabolism such as fatty liver, cholestasis, primary biliary cirrhosis, carnitine deficiency, carnitine palmitoyltransferase deficiency, myoadenylate deaminase deficiency, hypertriglyceridemia, lipid storage disorders such Fabry's disease, Gaucher's disease, Niemann-Pick's disease, metachromatic leukodystrophy, adrenoleukodystrophy, GM₂ gangliosidosis, and ceroid lipofuscinosis, abetalipoproteinemia, Tangier disease, hyperlipoproteinemia, diabetes mellitus, lipodystrophy, lipomatoses, acute panniculitis, disseminated fat necrosis, adiposis dolorosa, lipoid adrenal hyperplasia, minimal change disease, lipomas, atherosclerosis, hypercholesterolemia, hypercholesterolemia with hypertriglyceridemia, primary hypoalphalipoproteinemia, hypothyroidism, renal disease, liver disease, lecithin:cholesterol acyltransferase deficiency, cerebrotendinous xanthomatosis, sitosterolemia, hypocholesterolemia, Tay-Sachs disease, Sandhoff's disease, hyperlipidemia, hyperlipemia, lipid myopathies, and obesity; and disorders of copper metabolism such as Menke's disease, Wilson's disease, and Ehlers-Danlos syndrome type IX; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorder of the central nervous system, cerebral palsy, a neuroskeletal disorder, an autonomic nervous system disorder, a cranial nerve disorder, a spinal cord disease, muscular dystrophy and other neuromuscular disorder, a peripheral nervous system disorder, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathy, myasthenia gravis, periodic paralysis, a mental disorder including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, and Tourette's disorder; a gastrointestinal disorder including ulcerative colitis, gastric and duodenal ulcers, cystinuria, dibasicaminoaciduria, hypercystinuria, lysinuria, hartnup disease, tryptophan malabsorption, methionine malabsorption, histidinuria, iminoglycinuria, dicarboxylicaminoaciduria, cystinosis, renal glycosuria, hypouricemia, familial hypophophatemic rickets, congenital chloridorrhea, distal renal tubular acidosis, Menkes' disease, Wilson's disease, lethal diarrhea, juvenile pernicious anemia, folate malabsorption, adrenoleukodystrophy, hereditary myoglobinuria, and Zellweger syndrome; a transport disorder such as akinesia, amyotrophic lateral sclerosis, ataxia telangiectasia, cystic fibrosis, Becker's muscular dystrophy, Bell's palsy, Charcot-Marie Tooth disease, diabetes mellitus, diabetes insipidus, diabetic neuropathy, Duchenne muscular dystrophy, hyperkalemic periodic paralysis, normokalemic periodic paralysis, Parkinson's disease, malignant hyperthermia, multidrug resistance, myasthenia gravis, myotonic dystrophy, catatonia, tardive dyskinesia, dystonias, peripheral neuropathy, cerebral neoplasms, prostate cancer, cardiac disorders associated with transport, e.g., angina, bradyarrythmia, tachyarrythmia, hypertension, Long QT syndrome, myocarditis, cardiomyopathy, nemaline myopathy, centronuclear myopathy, lipid myopathy, mitochondrial myopathy, thyrotoxic myopathy, ethanol myopathy, dermatomyositis, inclusion body myositis, infectious myositis, and polymyositis, neurological disorders associated with transport, e.g., Alzheimer's disease, amnesia, bipolar disorder, dementia, depression, epilepsy, Tourette's disorder, paranoid psychoses, and schizophrenia, and other disorders associated with transport, e.g., neurofibromatosis, postherpetic neuralgia, trigeminal neuropathy, sarcoidosis, sickle cell anemia, cataracts, infertility, pulmonary artery stenosis, sensorineural autosomal deafness, hyperglycemia, hypoglycemia, Grave's disease, goiter, glucose-galactose malabsorption syndrome, hypercholesterolemia, Cushing's disease, and Addison's disease; and a connective tissue disorder such as osteogenesis imperfecta, Ehlers-Danlos syndrome, chondrodysplasias, Marfan syndrome, Alport syndrome, familial aortic aneurysm, achondroplasia, mucopolysaccharidoses, osteoporosis, osteopetrosis, Paget's disease, rickets, osteomalacia, hyperparathyroidism, renal osteodystrophy, osteonecrosis, osteomyelitis, osteoma, osteoid osteoma, osteoblastoma, osteosarcoma, osteochondroma, chondroma, chondroblastoma, chondromyxoid fibroma, chondrosarcoma, fibrous cortical defect, nonossifying fibroma, fibrous dysplasia, fibrosarcoma, malignant fibrous histiocytoma, Ewing's sarcoma, primitive neuroectodermal tumor, giant cell tumor, osteoarthritis, rheumatoid arthritis, ankylosing spondyloarthritis, Reiter's syndrome, psoriatic arthritis, enteropathic arthritis, infectious arthritis, gout, gouty arthritis, calcium pyrophosphate crystal deposition disease, ganglion, synovial cyst, villonodular synovitis, systemic sclerosis, Dupuytren's contracture, hepatic fibrosis, lupus erythematosus, mixed connective tissue disease, epidermolysis bullosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, pachyonychia congenita, and white sponge nevus. The dithp can be used to detect the presence of, or to quantify the amount of, a dithp-related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is established. Alternatively, a polynucleotide complementary to a given dithp can inhibit or inactivate a therapeutically relevant gene related to the dithp.

[0703] Analysis of dithp Expression Patterns

[0704] The expression of dithp may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of dithp expression. For example, the level of expression of dithp may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments. This type of analysis is useful, for example, to assess the relative levels of dithp expression in fully or partially differentiated cells or tissues, to determine if changes in dithp expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies. Methods for the analysis of dithp expression are based on hybridization and amplification technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.

[0705] Hybridization and Genetic Analysis

[0706] The dithp, their fragments, or complementary sequences, may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences. The dithp may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concentrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the dithp allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the dithp of the Sequence Listing. Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO:1-52 and tested for their ability to identify or amplify the target nucleic acid sequence using standard protocols.

[0707] Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ ID NO:1-52 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in “Definitions.”

[0708] A probe for use in Southern or northern hybridization may be derived from a fragment of a dithp sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing dithp. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression. An array analogous to a dot or slot blot may be used to arrange and link polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures. Such an array may contain any number of dithp and may be produced by hand or by using available devices, materials, and machines.

[0709] Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; and Heller, M. J. et al. (1997) U.S. Pat. No. 5,605,662.)

[0710] Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules. For example, commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaline phosphatase labeling (Life Technologies). Alternatively, dithp may be cloned into commercially available vectors for the production of RNA probes. Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., ³²P-ATP, Amersham Pharmacia Biotech).

[0711] Additionally the polynucleotides of SEQ ID NO:1-52 or suitable fragments thereof can be used to isolate full length cDNA sequences utilizing hybridization and/or amplification procedures well known in the art, e.g., cDNA library screening, PCR amplification, etc. The molecular cloning of such full length cDNA sequences may employ the method of cDNA library screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra, Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate genomic sequences of dithp in order to analyze, e.g., regulatory elements.

[0712] Genetic Mapping

[0713] Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder. For example, cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies, Alzheimer's disease has been linked to a gene on chromosome 21; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage anaiysis to physical mapping.

[0714] As a condition is noted among members of a family, a genetic linkage map traces parts of chromosomes that are inherited in the same pattern as the condition. Statistics link the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers. (See, for example, Lander, E. S. and Botstein, D. (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357.) Occasionally, genetic markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site.

[0715] In another embodiment of the invention, dithp sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or noncoding sequences of dithp may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a dithp coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (IACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries. (See, e.g., Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355; Price, C. M. (1993) Blood Rev. 7:127-134; and Trask, B. J. (1991) Trends Genet. 7:149-154.)

[0716] Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Meyers, supra, pp. 965-968.) Correlation between the location of dithp on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder. The dithp sequences may also be used to detect polymorphisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.

[0717] In situ hybridization of chromosomal preparations and genetic mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic linkage with a particular genomic region, e.g., ataxia-telangiectasia to 11q22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti, R. A. et al. (1988) Nature 336:577-580.) The nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.

[0718] Once a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease. This process requires a physical map of the chromosomal region containing the disease-gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods.

[0719] Diagnostic Uses

[0720] The dithp of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of dithp expression. Labeled probes developed from dithp sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, dithp, or fragments or oligonucleotides derived from dithp, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If dithp expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease. Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent assay (ELISA)-like, pin, or chip-based assays.

[0721] The probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of dithp expression, or to evaluate the efficacy of a particular therapeutic treatment. The candidate probe may be identified from the dithp that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.

[0722] The polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA. The polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples.

[0723] In a particular aspect, oligonucleotide primers derived from the dithp of the invention may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from the polynucleotide sequences encoding DITHP are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymorphisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego Calif.).

[0724] DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids; e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992) PCR Technology, Freeman and Co., New York, N.Y.). Similarly, polynucleotides of the present invention can be used as polymorphic markers.

[0725] There is also a need for reagents capable of identifying the source of a particular tissue. Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.

[0726] The polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a particular cell type, in the creation of subtracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, and as an antigen to elicit an immune response.

[0727] Disease Model Systems Using ditp,

[0728] The dithp of the invention or their mammalian homologs may be “knocked out” in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Pat. Nos. 5,175,383 and 5,767,337.) For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M. R. (1989) Science 244:1288-1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J. D. (1996) Clin. Invest. 97:1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.

[0729] The dithp of the invention may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J. A. et al. (1998) Science 282:1145-1147).

[0730] The dithp of the invention can also be used to create “knockin” humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of dithp is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress dithp, resulting, e.g., in the secretion of DITHP in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

[0731] Screening Assays

[0732] DITHP encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.

[0733] Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic. (See, Coligan et al., (1991) Current Protocols in Immunology 1(2): Chapter 5.) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques. Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.

[0734] An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.

[0735] Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.

[0736] Preferably, an ELISA assay using, e.g., a monoclonal or polyclonal antibody, can measure polypeptide level in a sample. The antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.

[0737] All of the above assays can be used in a diagnostic or prognostic context. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.

[0738] Transcript Imaging

[0739] Another embodiment relates to the use of dithp to develop a transcript image of a tissue or cell type. A transcript image is the collective pattern of gene expression by a particular tissue or cell type under given conditions and at a given time. This pattern of gene expression is defined by the number of expressed genes, their abundance, and their function. Thus the dithp of the present invention may be used to develop a transcript image of a tissue or cell type by hybridizing, preferably in a microarray format, the dithp of the present invention to the totality of transcripts or reverse transcripts of a tissue or cell type. The resultant transcript image would provide a profile of gene activity pertaining to human molecules for diagnostics and therapeutics.

[0740] Transcript images which profile dithp expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect dithp expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line. Transcript images may be used to profile dithp expression in distinct tissue types. This process can be used to determine the activity of human diagnostic and therapeutic molecules in a particular tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of dithp expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used for diagnostic purposes, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect the activity of human diagnostic and therapeutic molecules.

[0741] Transcript images which profile dithp expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals. Transcript images of cell lines can be used to assess the activity of human diagnostic and therapeutic molecules and/or to identify cell lines that lack or misregulate this activity. Such cell lines may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in the activity of human diagnostic and therapeutic molecules. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.

[0742] Antisense Molecules

[0743] The polynucleotides of the present invention are useful in antisense technology. Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression. (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa N.J.; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S. T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H. W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med. 62(1):11-22.) An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J. J. et al. (1991) Antisense Res. Dev. 1(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W. M. et al. (1995) Proc. Natl. Acad. Sci. USA 92(12):5592-5596; and Nielsen, P. E. and Haaima, G. (1997) Chem. Soc. Rev. 96:73-78.) Typically, the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs. Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double helix.

[0744] The polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by dithp. The antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (PE Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of interest. (See, e.g., Agrawal, supra.)

[0745] In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J. E., et al. (1998) J. Allergy Clin. Immunol. 102(3):469-475; and Scanlon, K. J., et al. (1995) 9(13):1288-1296.) Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors. (See, e.g., Miller, A. D. (1990) Blood 76:271; Ausubel, F. M. et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g., Rossi, J. J. (1995) Br. Med. Bull. 51(1):217-225; Boado, R. J. et al. (1998) J. Pharm. Sci. 87(11):1308-1315; and Morris, M. C. et al. (1997) Nucleic Acids Res. 25(14):2730-2736.)

[0746] Expression

[0747] In order to express a biologically active DITHP, the nucleotide sequences encoding DITHP or fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding DITHP and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra, Chapters 4, 8, 16, and 17; and Ausubel, supra, Chapters 9, 10, 13, and 16.)

[0748] A variety of expression vector/host systems may be utilized to contain and express sequences encoding DITHP. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems. (See, e.g., Sambrook, supra; Ausubel, 1995, supra, Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; Scorer, C. A. et al. (1994) Bio/Technology 12:181-184; Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355.) Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al., (1993) Proc. Natl. Acad. Sci. USA 90(13):6340-6344; Buller, R. M. et al. (1985) Nature 317(6040):813-815; McGregor, D. P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, I. M. and N. Somia (1997) Nature 389:239-242.) The invention is not limited by the host cell employed.

[0749] For long term production of recombinant proteins in mammalian systems, stable expression of DITHP in cell lines is preferred. For example, sequences encoding DITHP can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover transformed cell lines. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14; Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051; Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131.)

[0750] Therapeutic Uses of dithp

[0751] The dithp of the invention may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al. (1995) Science 270:475-480; Bordignon, C. et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207-216; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:667-703), thalassemias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, R. G. (1995) Science 270:404-410; Verma, I. M. and Somia, N. (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA. 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as Plasmodium falciparum and Trypanosoma cruzi). In the case where a genetic deficiency in dithp expression or regulation causes disease, the expression of dithp from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.

[0752] In a further embodiment of the invention, diseases or disorders caused by deficiencies in dithp are treated by constructing mammalian expression vectors comprising dithp and introducing these vectors by mechanical means into dithp-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R. A. and Anderson, W. F. (1993) Annu. Rev. Biochem. 62:191-217; Ivics, Z. (1997) Cell 91:501-510; Boulay, J-L. and Récipon, H. (1998) Curr. Opin. Biotechnol. 9:445-450).

[0753] Expression vectors that may be effective for the expression of dithp include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad Calif.), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla Calif.), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto Calif.). The dithp of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter (e.g., the tetracycline-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Natl. Acad. Sci. U.S.A. 89:5547-5551; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F. M. V. and Blau, H. M. (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen)); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F. M. V. and Blau, H. M. supra)), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding DITHP from a normal individual.

[0754] Commercially available liposome transformation kits (e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F. L. and Eb, A.J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.

[0755] In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to dithp expression are treated by constructing a retrovirus vector consisting of (i) the dithp of the invention under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92:6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M. A. et al. (1987) J. Virol. 61:1639-1646; Adam, M. A. and Miller, A. D. (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Pat. No. 5,910,434 to Rigg (“Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant”) discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4⁺ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:1201-1206; Su, L. (1997) Blood 89:2283-2290).

[0756] In the alternative, an adenovirus-based gene therapy delivery system is used to deliver dithp to cells which have one or more genetic abnormalities with respect to the expression of dithp. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M. E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Pat. No. 5,707,618 to Armentano (“Adenovirus vectors for gene therapy”), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P. A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, I. M. and Somia, N. (1997) Nature 18:389:239-242, both incorporated by reference herein.

[0757] In another alternative, a herpes-based, gene therapy delivery system is used to deliver dithp to target cells which have one or more genetic abnormalities with respect to the expression of dithp. The use of herpes simplex virus (HSV)-based vectors may be especially valuable for introducing dithp to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res. 169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Pat. No. 5,804,413 to DeLuca (“Herpes simplex virus strains for gene transfer”), which is hereby incorporated by reference. U.S. Pat. No. 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. 1999 J. Virol. 73:519-532 and Xu, H. et al., (1994) Dev. Biol. 163:152-161, hereby incorporated by reference. The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of herpesvirus, and the infection of cells with herpesvirus are techniques well known to those of ordinary skill in the art.

[0758] In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver dithp to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and Li, K-J. (1998) Curr. Opin. Biotech. 9:464-469). During alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA replicates to higher levels than the full-length genomic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting dithp into the alphavirus genome in place of the capsid-coding region results in the production of a large number of dithp RNAs and the synthesis of high levels of DITHP in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S. A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of DITIHP into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.

[0759] Antibodies

[0760] Anti-DITHP antibodies may be used to analyze protein expression levels. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound, J. D. (1998) Immunochemical Protocols, Humana Press, Totowa, N.J.

[0761] The amino acid sequence encoded by the dithp of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity. The optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophilic regions of the polypeptide which are likely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select appropriate epitopes is also described by Ausubel (1997, supra, Chapter 11.7). Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic. Peptides used to induce specific antibodies may have an amino acid sequence consisting of at five amino acids, preferably at least 10 amino acids, and most preferably 15 amino acids. A peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole limpet cyanin (KLH; Sigma, St. Louis Mo.) for antibody production. A peptide encompassing an antigenic region may be expressed from a dithp, synthesized as described above, or purified from human cells.

[0762] Procedures well known in the art may be used for the production of antibodies. Various hosts including mice, goats, and rabbits, may be immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.

[0763] In one procedure, peptides about 15 residues in length may be synthesized using an ABI 431A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, supra). Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1% bovine serum albumin (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.

[0764] In another procedure, isolated and purified peptide may be used to immunize mice (about 100 μg of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is sufficient for labeling and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody. In a typical protocol, wells of a multi-well plate (FAST, Becton-Dickinson, Palo Alto, Calif.) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mg/ml. The coated wells are blocked with 1% BSA and washed and exposed to supernatants from hybridomas. After incubation, the wells are exposed to radiolabeled peptide at 1 mg/ml.

[0765] Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and-immunoblotting.

[0766] Antibody fragments containing specific binding sites for an epitope may also be generated. For example, such fragments include, but are not limited to, the F(ab′)2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, construction of Fab expression libraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity (Pound, supra, Chaps. 45-47). Antibodies generated against polypeptide encoded by dithp can be used to purify and characterize full-length DITHP protein and its activity, binding partners, etc.

[0767] Assays Using Antibodies

[0768] Anti-DITHP antibodies may be used in assays to quantify the amount of DITHP found in a particular human cell. Such assays include methods utilizing the antibody and a label to detect expression level under normal or disease conditions. The peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.

[0769] Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell sorting (FACS). Such immunoassays typically involve the formation of complexes between the DITHP and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).

[0770] Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

[0771] The disclosures of all patents, applications, and publications mentioned above and below, in particular U.S. Ser. Nos. 60/137,109, 60/137,337, 60/137,258, 60/137,260, 60/137,113, 60/137,161, 60/137,417, 60/137,259, 60/137,396, 60/137,114, 60/137,173, 60/137,411, 60/147,436, 60/147,549, 60/147,377, 60/147,527, 60/147,520, 60/147,536, 60/147,530, 60/147,547, 60/147,824, 60/147,541, 60/147,542, and 60/147,500, are hereby expressly incorporated by reference.

EXAMPLES

[0772] I. Construction of cDNA Libraries

[0773] RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto Calif.) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.

[0774] Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In most cases, RNA was treated with DNase. For most libraries, poly(A+) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega Corporation (Promega), Madison Wis.), OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia Calif.), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Inc., Austin Tex.).

[0775] In some cases, Stratagene was provided with RNA and constructed the corresponding cDNA libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene Cloning Systems, Inc. (Stratagene), La Jolla Calif.) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, Chapters 5.1 through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), pSPORT1 plasmid (Life Technologies), or pINCY (Incyte). Recombinant plasmids were transformed into competent E. coli cells including XL1-Blue, XL1-BlueMRF, or SOLR from Stratagene or DH5α, DH10B, or ElectroMAX DH10B from Life Technologies.

[0776] II. Isolation of cDNA Clones

[0777] Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg Md.); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4° C.

[0778] Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format. (Rao, V. B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene Oreg.) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

[0779] III. Sequencing and Analysis

[0780] cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (PE Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Corp., Sunnyvale Calif.) or the MICROLAB 2200 liquid transfer system (Hamilton). cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (PE Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, Chapter 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.

[0781] IV. Assembly and Analysis of Sequences

[0782] Component sequences from chromatograms were subject to PHRED analysis and assigned a quality score. The sequences having at least a required quality score were subject to various pre-processing editing pathways to eliminate, e.g., low quality 3′ ends, vector and linker sequences, poly A tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. In particular, low-information sequences and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) were replaced by “n's”, or masked, to prevent spurious matches.

[0783] Processed sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quality score greater than or equal to 150. Alignments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation (sense or antisense) of each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence listing correspond to sense strand sequences (the “forward” reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein. The component sequences which were used to assemble each template consensus sequence are listed in Table 4, along with their positions along the template nucleotide sequences.

[0784] Bins were compared against each other and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-split. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures.

[0785] Once gene bins were generated based upon sequence alignments, bins were clone joined based upon clone information. If the 5′ sequence of one clone was present in one bin and the 3′ sequence from the same clone was present in a different bin, it was likely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.

[0786] The final assembled templates were subsequently annotated using the following procedure. Template sequences were analyzed using BLASTn (v2.0, NCBI) versus gbpri (GenBank version 116). “Hits” were defined as an exact match having from 95% local identity over 200 base pairs through 100% local identity over 100 base pairs, or a homolog match having an E-value, i.e. a probability score, of ≦1×10⁻⁸. The hits were subject to frameshift FASTx versus GENPEPT (GenBank version 116). (See Table 5). In this analysis, a homolog match was defined as having an E-value of ≦1×10⁻⁸. The assembly method used above was described in “System and Methods for Analyzing Biomolecular Sequences,” U.S. Ser. No. 09/276,534, filed Mar. 25, 1999, and the LIFESEQ Gold user manual (Incyte) both incorporated by reference herein.

[0787] Following assembly, template sequences were subjected to motif, BLAST, and functional analyses, and categorized in protein hierarchies using methods described in, e.g., “Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data,” U.S. Ser. No. 08/812,290, filed Mar. 6, 1997; “Relational Database for Storing Biomolecule Information,” U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; “Project-Based Full-Length Biomolecular Sequence Database,” U.S. Ser. No. 08/811,758, filed Mar. 6, 1997; and “Relational Database and System for Storing Information Relating to Biomolecular Sequences,” U.S. Ser. No. 09/034,807, filed Mar. 4, 1998, all of which are incorporated by reference herein.

[0788] The template sequences were further analyzed by translating each template in all three forward reading frames and searching each translation against the Pfam database of hidden Markov model-based protein families and domains using the HMMER software package (available to the public from Washington University School of Medicine, St. Louis Mo.). Regions of templates which, when translated, contain similarity to Pfam consensus sequences are reported in Table 2, along with descriptions of Pfam protein domains and families. Only those Pfam hits with an E-value of ≦1×10⁻³ are reported. (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and families.)

[0789] Additionally, the template sequences were translated in all three forward reading frames, and each translation was searched against hidden Markov models for signal peptide and transmembrane domains using the HMMER software package. Construction of hidden Markov models and their usage in sequence analysis has been described. (See, for example, Eddy, S. R. (1996) Curr. Opin. Str. Biol. 6:361-365.) Regions of templates which, when translated, contain similarity to signal peptide or transmembrane domain consensus sequences are reported in Table 3. Only those signal peptide or transmembrane hits with a cutoff score of 11 bits or greater are reported. A cutoff score of 11 bits or greater corresponds to at least about 91-94% true-positives in signal peptide prediction, and at least about 75% true-positives in transmembrane domain prediction.

[0790] The results of HMMER analysis as reported in Tables 2 and 3 may support the results of BLAST analysis as reported in Table 1 or may suggest alternative or additional properties of template-encoded polypeptides not previously uncovered by BLAST or other analyses.

[0791] Template sequences are further analyzed using the bioinformatics tools listed in Table 5, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco Calif.) and LASERGENE software (DNASTAR). Template sequences may be further queried against public databases such as the GenBank rodent, mammalian, vertebrate, prokaryote, and eukaryote databases.

[0792] V. Analysis of Polynucleotide Expression

[0793] Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)

[0794] Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Pharmaceuticals). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as: $\frac{{BLAST}\quad {Score} \times {Percent}\quad {Identity}}{5 \times {minimum}{\quad \quad}\left\{ {{{length}\quad \left( {{Seq}.\quad 1} \right)},{{length}\quad \left( {{Seq}.\quad 2} \right)}} \right\}}$

[0795] The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and −4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.

[0796] VI. Tissue Distribution Profiling

[0797] A tissue distribution profile is determined for each template by compiling the cDNA library tissue classifications of its component cDNA sequences. Each component sequence, is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract. Template sequences, component sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.).

[0798] VII. Transcript Image Analysis

[0799] Transcript images are generated as described in Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No. 5,840,484, incorporated herein by reference.

[0800] VIII. Extension of Polynucleotide Sequences and Isolation of a Full-length cDNA

[0801] Oligonucleotide primers designed using a dithp of the Sequence Listing are used to extend the nucleic acid sequence. One primer is synthesized to initiate 5′ extension of the template, and the other primer, to initiate 3′ extension of the template. The initial primers may be designed using OLIGO 4.06 software (National Biosciences, Inc. (National Biosciences), Plymouth Min.), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations are avoided. Selected human cDNA libraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.

[0802] High fidelity amplification is obtained by PCR using methods well known in the art. PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research)., The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg²⁺, (NH₄)₂SO₄, and β-mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 68° C. 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C.

[0803] The concentration of DNA in each well is determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in 1×Tris-EDTA (TE) and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Incorporated (Corning), Corning N.Y.), allowing the DNA to bind to the reagent. The plate is scanned in a FLUOROSKAN II (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture is analyzed by electrophoresis on a 1% agarose mini-gel to determine which reactions are successful in extending the sequence.

[0804] The extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega). Extended clones are religated using T4 ligase (New England Biolabs, Inc., Beverly Mass.) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37° C. in 384-well plates in LB/2×carbenicillin liquid media.

[0805] The cells are lysed, and DNA is amplified by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C. DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems).

[0806] In like manner, the dithp is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oligonucleotides designed for such extension, and an appropriate genomic library.

[0807] IX. Labeling of Probes and Southern Hybridization Analyses

[0808] Hybridization probes derived from the dithp of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeling of probe nucleotides between 100 and 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments. Probe sequences are labeled at room temperature for 30 minutes using a T4 polynucleotide kinase, γ³²P-ATP, and 0.5× One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to 10⁷ dpm/μg/ml hybridization buffer and used in a typical membrane-based hybridization analysis.

[0809] The DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed through a 0.7% agarose gel. The DNA fragments are transferred from the agarose to nylon membrane (NYTRAN Plus, Schleicher & Schuell, Inc., Keene N. H.) using procedures specified by the manufacturer of the membrane. Prehybridization is carried out for three or more hours at 68° C., and hybridization is carried out overnight at 68° C. To remove non-specific signals, blots are sequentially washed at room temperature under increasingly stringent conditions, up to 0.1× saline sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA.

[0810] X. Chromosome Mapping of dithp

[0811] The cDNA sequences which were used to assemble SEQ ID NO:1-52 are compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that match SEQ ID NO: 1-52 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 5). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Généthon are used to determine if any of the clustered sequences have been previously mapped. Inclusion of a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location. The genetic map locations of SEQ ID NO:1-52 are described as ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Généthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters.

[0812] XI. Microarray Analysis

[0813] Probe Preparation from Tissue or Cell Samples

[0814] Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA⁺ RNA is purified using the oligo (dT) cellulose method. Each polyA⁺ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oligo-dT primer (21 mer), 1× first strand buffer, 0.03 units/Al RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng polyA⁺ RNA with GEMBRIGHT kits (Incyte). Specific control polyA⁺ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpublished). As quantitative controls, the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse transcription reaction at ratios of 1:100,000, 1:10,000, 1:1000, 1:100 (w/w) to sample mRNA respectively. The control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37° C. for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C. to the stop the reaction and degrade the RNA. Probes are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto Calif.) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2% SDS.

[0815] Microarray Preparation

[0816] Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 μg. Amplified array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).

[0817] Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester, Pa.), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110° C. oven.

[0818] Array elements are applied to the coated glass substrate using a procedure described in U.S. Pat. No. 5,807,522, incorporated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide.

[0819] Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saline (PBS) (Tropix, Inc., Bedford, Mass.) for 30 minutes at 60° C. followed by washes in 0.2% SDS and distilled water as before.

[0820] Hybridization

[0821] Hybridization reactions contain 9 μl of probe mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5×SSC, 0.2% SDS hybridization buffer. The probe mixture is heated to 65° C. for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cm² coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5×SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C. in a first wash buffer (1×SSC, 0.1% SDS), three times for 10 minutes each at 45° C. in a second wash buffer (0.1×SSC), and dried.

[0822] Detection

[0823] Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara Calif.) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20× microscope objective (Nikon, Inc., Melville N.Y.). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm×1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.

[0824] In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially. Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.

[0825] The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000. When two probes from different is sources (e.g., representing test and control cells), each labeled with a different fluorophore, are hybridized to a single array for the purpose of identifying genes that are differentially expressed, the calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.

[0826] The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, Mass.) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

[0827] A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).

[0828] XII. Complementary Nucleic Acids

[0829] Sequences complementary to the dithp are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide. The use of oligonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used. Appropriate oligonucleotides are designed from the dithp using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial supplier. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent transcription factor binding to the promoter sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.

[0830] XIII. Expression of DITHP

[0831] Expression and purification of DITHP is accomplished using bacterial or virus-based expression systems. For expression of DITHP in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3). Antibiotic resistant bacteria express DITHP upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expression of DITHP in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding DITHP by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, supra; and Sandig, supra.)

[0832] In most expression systems, DITHP is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma japonicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from DITHP at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak Company, Rochester N.Y.). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, Chapters 10 and 16). Purified DITHP obtained by these methods can be used directly in the following activity assay.

[0833] XIV. Demonstration of DITHP Activity

[0834] DITHP activity is demonstrated through a variety of specific assays, some of which are outlined below.

[0835] Oxidoreductase activity of DITHP is measured by the increase in extinction coefficient of NAD(P)H coenzyme at 340 nm for the measurement of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nm for the measurement of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858). One of three substrates may be used: Asn-βGal, biocytidine, or ubiquinone-10. The respective subunits of the enzyme reaction, for example, cytochtome c₁-b oxidoreductase and cytochrome c, are reconstituted. The reaction mixture-contains a)1-2 mg/ml DITHP; and b) 15 mM substrate, 2.4 mM NAD(P)⁺ in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na₂HPO₄ buffer, pH 7.4 (reduction reaction); in a total volume of 0.1 ml. Changes in absorbance at 340 nm (A₃₄₀) are measured at 23.5° C. using a recording spectrophotometer (Shimadzu Scientific Instruments, Inc., Pleasanton Calif.). The amount of NAD(P)H is stoichiometrically equivalent to the amount of substrate initially present, and the change in A₃₄₀ is a direct measure of the amount of NAD(P)H produced; ΔA₃₄₀ =6620[NADH]. Oxidoreductase activity of DITHP activity is proportional to the amount of NAD(P)H present in the assay.

[0836] Transferase activity of DITHP is measured through assays such as a methyl transferase assay in which the transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate is measured (Bokar, J. A. et al. (1994) J. Biol. Chem. 269:17697-17704). Reaction mixtures (50 μl final volume) contain 15 mM BEPES, pH 7.9, 1.5 mM MgCl₂, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [methyl-³H]AdoMet (0.375 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, and acceptor substrate (0.4 μg [³⁵S]RNA or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30° C. for 30 minutes, then 65° C. for 5 minutes. The products are separated by chromatography or electrophoresis and the level of methyl transferase activity is determined by quantification of methyl-³H recovery.

[0837] DITHP hydrolase activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotometric (or fluorometric) absorption of the released chromophore. (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York N.Y., pp. 25-55) Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases), animopeptidase (leucine aminopeptidase), or carboxypeptidase (Carboxypeptidase A and B, procollagen C-proteinase).

[0838] DITHP isomerase activity such as peptidyl prolyl cis/trans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J. U., et al. (1994) (FEBS Lett. 352: 180-184). The assay is performed at 10° C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and DITHP at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 ul) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above. Only the cis isomer of the substrate is a substrate for cleavage by chymotrypsin. Thus, as the substrate is isomerized by DITHP, the product is cleaved by chymotrypsin to produce 4-nitroanilide, which is detected by it's absorbance at 390 nm. 4-Nitroanilide appears in a time-dependent and a DITHP concentration-dependent manner.

[0839] An assay for DITHP activity associated with growth and development measures cell proliferation as the amount of newly initiated DNA synthesis in Swiss mouse 3T3 cells. A plasmid containing polynucleotides encoding DITHP is transfected into quiescent 3T3 cultured cells using methods well known in the art. The transiently transfected cells are then incubated in the presence of [³H]thymidine, a radioactive DNA precursor. Where applicable, varying amounts of DITHP ligand are added to the transfected cells. Incorporation of [³H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA.

[0840] Growth factor activity of DITHP is measured by the stimulation of DNA synthesis in Swiss mouse 3T3 cells (McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford University Press, New York N.Y.). Initiation of DNA synthesis indicates the cells' entry into the mitotic cycle and their commitment to undergo later division. 3T3 cells are competent to respond to most growth factors, not only those that are mitogenic, but also those that are involved in embryonic induction. This competence is possible because the in vivo specificity demonstrated by some growth factors is not necessarily inherent but is determined by the responding tissue. In this assay, varying amounts of DITHP are added to quiescent 3T3 cultured cells in the presence of [³H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incorporation of [³H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP concentration range is indicative of growth factor activity. One unit of activity per milliliter is defined as the concentration of DITHP producing a 50% response level, where 100% represents maximal incorporation of [³H]thymidine into acid-precipitable DNA.

[0841] Alternatively, an assay for cytokine activity of DITHP measures the proliferation of leukocytes. In this assay, the amount of tritiated thymidine incorporated into newly synthesized DNA is used to estimate proliferative activity. Varying amounts of DITHP are added to cultured leukocytes, such as granulocytes, monocytes, or lymphocytes, in the presence of [³H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incorporation of [³H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP concentration range is indicative of DITHP activity. One unit of activity per milliliter is conventionally defined as the concentration of DITHP producing a 50% response level, where 100% represents maximal incorporation of [³H]thymidine into acid-precipitable DNA.

[0842] An alternative assay for DITHP cytokine activity utilizes a Boyden micro chamber (Neuroprobe, Cabin John MD) to measure leukocyte chemotaxis (Vicari, supra). In this assay, about 10⁵ migratory cells such as macrophages or monocytes are placed in cell culture media in the upper compartment of the chamber. Varying dilutions of DITHP are placed in the lower compartment. The two compartments are separated by a 5 or 8 micron pore polycarbonate filter (Nucleopore, Pleasanton Calif.). After incubation at 37° C. for 80 to 120 minutes, the filters are fixed in methanol and stained with appropriate labeling agents. Cells which migrate to the other side of the filter are counted using standard microscopy. The chemotactic index is calculated by dividing the number of migratory cells counted when DITHP is present in the lower compartment by the number of migratory cells counted when only media is present in the lower compartment. The chemotactic index is proportional to the activity of DITHP.

[0843] Alternatively, cell lines or tissues transformed with a vector containing dithp can be assayed for,DITHP activity by immunoblotting. Cells are denatured in SDS in the presence of β-mercaptoethanol, nucleic acids removed by ethanol precipitation, and proteins purified by acetone precipitation. Pellets are resuspended in 20 mM tris buffer at pH 7.5 and incubated with Protein G-Sepharose pre-coated with an antibody specific for DITHP. After washing, the Sepharose beads are boiled in electrophoresis sample buffer, and the eluted proteins subjected to SDS-PAGE. The SDS-PAGE is transferred to a nitrocellulose membrane for immunoblotting, and the DITHP activity is assessed by visualizing and quantifying bands on the blot using the antibody specific for DITHP as the primary antibody and ¹²⁵I-labeled IgG specific for the primary antibody as the secondary antibody.

[0844] DITHP kinase activity is measured by phosphorylation of a protein substrate using γ-labeled [³²P]-ATP and quantitation of the incorporated radioactivity using a radioisotope counter. DITHP is incubated with the protein substrate, [³²P]-ATP, and an appropriate kinase buffer. The [³²P] incorporated into the product is separated from free [³²P]-ATP by electrophoresis and the incorporated [³²P] is counted. The amount of [³²P] recovered is proportional to the kinase activity of DITHP in the assay. A determination of the specific amino acid residue phosphorylated is made by phosphoamino acid analysis of the hydrolyzed protein.

[0845] In the alternative, DITHP activity is measured by the increase in cell proliferation resulting from transformation of a mammalian cell line such as COS7, HeLa or CHO with an eukaryotic expression vector encoding DITHP. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression of DITHP. Phase microscopy is then used to compare the mitotic index of transformed versus control cells. An increase in the mitotic index indicates DITHP activity.

[0846] In a further alternative, an assay for DITHP signaling activity is based upon the ability of GPCR family proteins to modulate G protein-activated second messenger signal transduction pathways (e.g., cAMP; Gaudin, P. et al. (1998) J. Biol. Chem. 273:4990-4996). A plasmid encoding full length DITHP is transfected into a mammalian cell line (e.g., Chinese hamster ovary (CHO) or human embryonic kidney (HEK-293) cell lines) using methods well-known in the art. Transfected cells are grown in 12-well trays in culture medium for 48 hours, then the culture medium is discarded, and the attached cells are gently washed with PBS. The cells are then incubated in culture medium with or without ligand for 30 minutes, then the medium is removed and cells lysed by treatment with 1 M perchloric acid. The cAMP levels in the lysate are measured by radioimmunoassay using methods well-known in the art. Changes in the levels of cAMP in the lysate from cells exposed to ligand compared to those without ligand are proportional to the amount of DITHP present in the transfected cells.

[0847] Alternatively, an assay for DITHP protein phosphatase activity measures the hydrolysis of P-nitrophenyl phosphate (PNPP). DITHP is incubated together with PNPP in HEPES buffer pH 7.5, in the presence of 0.1% β-mercaptoethanol at 37° C. for 60 min. The reaction is stopped by the addition of 6 ml of 10 N NaOH, and the increase in light absorbance of the reaction mixture at 410 nm resulting from the hydrolysis of PNPP is measured using a spectrophotometer. The increase in light absorbance is proportional to the phosphatase activity of DITHP in the assay (Diamond, R. H. et al (1994) Mol Cell Biol 14:3752-3762).

[0848] An alternative assay measures DITHP-mediated G-protein signaling activity by monitoring the mobilization of Ca⁺⁺ as an indicator of the signal transduction pathway stimulation. (See, e.g., Grynkievicz, G. et al. (1985) J. Biol. Chem. 260:3440; McColl, S. et al. (1993) J. Immunol. 150:4550-4555; and Aussel, C. et al. (1988) J. Immunol. 140:215-220). The assay requires preloading neutrophils or T cells with a fluorescent dye such as FURA-2 or BCECF (Universal Imaging Corp, Westchester Pa.) whose emission characteristics are altered by Ca⁺⁺ binding. When the cells are exposed to one or more activating stimuli artificially (e.g., anti-CD3 antibody ligation of the T cell receptor) or physiologically (e.g., by allogeneic stimulation), Ca⁺⁺ flux takes place. This flux can be observed and quantified by assaying the cells in a fluorometer or fluorescent activated cell sorter. Measurements of Ca⁺⁺ flux are compared between cells in their normal state and those transfected with DITHP. Increased Ca⁺⁺ mobilization attributable to increased DITHP concentration is proportional to DITHP activity.

[0849] DITHP transport activity is assayed by measuring uptake of labeled substrates into Xenopus laevis oocytes. Oocytes at stages V and VI are injected with DITHP mRNA (10 ng per oocyte) and incubated for 3 days at 18° C. in OR2 medium (82.5 mM NaCl, 2.5 mM KCT, 1 mM CaCl₂, 1 mM MgCl₂, 1 mM Na₂HPO₄, 5 mM Hepes, 3.8 mM NaOH, 50 μg/ml gentamycin, pH 7.8) to allow expression of DITHP protein. Oocytes are then transferred to standard uptake medium (100 mM NaCl, 2 mM KCl, 1 mM CaCl₂, 1 mM MgCl₂, 10 mM Hepes/Tris pH 7.5). Uptake of various substrates (e.g., amino acids, sugars, drugs, ions, and neurotransmitters) is initiated by adding labeled substrate (e.g. radiolabeled with ³H, fluorescently labeled with rhodamine, etc.) to the oocytes. After incubating for 30 minutes, uptake is terminated by washing the oocytes three times in Na⁺-free medium, measuring the incorporated label, and comparing with controls. DITHP transport activity is proportional to the level of internalized labeled substrate.

[0850] DITHP transferase activity is demonstrated by a test for galactosyltransferase activity. This can be determined by measuring the transfer of radiolabeled galactose from UDP-galactose to a GlcNAc-terminated oligosaccharide chain (Kolbinger, F. et al. (1998) J. Biol. Chem. 273:58-65). The sample is incubated with 14 μl of assay stock solution (180 mM sodium cacodylate, pH 6.5, 1 mg/ml bovine serum albumin, 0.26 mM UDP-galactose, 2 μl of UDP-[³H]galactose), 1 μl of MnCl₂ (500 mM), and 2.5 μl of GlcNAcβO-(CH₂)₈-CO₂Me (37 mg/ml in dimethyl sulfoxide) for 60 minutes at 37° C. The reaction is quenched by the addition of 1 ml of water and loaded on a C18 Sep-Pak cartridge (Waters), and the column is washed twice with 5 ml of water to remove unreacted UDP-[³H]galactose. The [³H]galactosylated GlcNAcβO-(CH₂)₈-CO₂Me remains bound to the column during the water washes and is eluted with 5 ml of methanol. Radioactivity in the eluted material is measured by liquid scintillation counting and is proportional to galactosyltransferase activity in the starting sample.

[0851] In the alternative, DITHP induction by heat or toxins may be demonstrated using primary cultures of human fibroblasts or human cell lines such as CCL-13, HEK293, or HEP G2 (ATCC). To heat induce DITHP expression, aliquots of cells are incubated at 42° C. for 15, 30, or 60 minutes. Control aliquots are incubated at 37° C. for the same time periods. To induce DITHP expression by toxins, aliquots of cells are treated with 100 μM arsenite or 20 mM azetidine-2-carboxylic acid for 0, 3, 6, or 12 hours. After exposure to heat, arsenite, or the amino acid analogue, samples of the treated cells are harvested and cell lysates prepared for analysis by western blot. Cells are lysed in lysis buffer containing 1% Nonidet P-40, 0.15 M NaCl, 50 mM Tris-HCl, 5 mM EDTA, 2 mM N-ethylmaleimide, 2 mM phenylmethylsulfonyl fluoride, 1 mg/ml leupeptin, and 1 mg/ml pepstatin. Twenty micrograms of the cell lysate is separated on an 8% SDS-PAGE gel and transferred to a membrane. After blocking with 5% nonfat dry milk/phosphate-buffered saline for 1 h, the membrane is incubated overnight at 4° C. or at room temperature for 2-4 hours with a 1:1000 dilution of anti-DITHP serum in 2% nonfat dry milk/phosphate-buffered saline. The membrane is then washed and incubated with a 1:1000 dilution of horseradish peroxidase-conjugated goat anti-rabbit IgG in 2% dry milk/phosphate-buffered saline. After washing with 0.1% Tween 20 in phosphate-buffered saline, the DITHP protein is detected and compared to controls using chemiluminescence.

[0852] Alternatively, DITHP protease activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotometric (or fluorometric) absorption of the released chromophore (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York, N.Y., pp.25-55). Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases, or metalloproteases), aminopeptidase (leucine aminopeptidase), or carboxypeptidase (carboxypeptidases A and B, procollagen C-proteinase). Commonly used chromogens are 2-naphthylamine, 4-nitroaniline, and furylacrylic acid. Assays are performed at ambient temperature and contain an aliquot of the enzyme and the appropriate substrate in a suitable buffer. Reactions are carried out in an optical cuvette, and the increase/decrease in absorbance of the chromogen released during hydrolysis of the peptide substrate is measured. The change in absorbance is proportional to the DITHP protease activity in the assay.

[0853] In the alternative, an assay for DITHP protease activity takes advantage of fluorescence resonance energy transfer (FRET) that occurs when one donor and one acceptor fluorophore with an appropriate spectral overlap are in close proximity. A flexible peptide linker containing a cleavage site specific for PRTS is fused between a red-shifted variant (RSGFP4) and a blue variant (BFP5) of Green Fluorescent Protein. This fusion protein has spectral properties that suggest energy transfer is occurring from BFP5 to RSGFP4. When the fusion protein is incubated with DITHP, the substrate is cleaved, and the two fluorescent proteins dissociate. This is accompanied by a marked decrease in energy transfer which is quantified by comparing the emission spectra before and after the addition of DITHP (Mitra, R. D. et al (1996) Gene 173:13-17). This assay can also be performed in living cells. In this case the fluorescent substrate protein is expressed constitutively in cells and DITHP is introduced on an inducible vector so that FRET can be monitored in the presence and absence of DITHP (Sagot, I. et al (1999) FEBS Lett. 447:53-57).

[0854] A method to determine the nucleic acid binding activity of DITHP involves a polyacrylamide gel mobility-shift assay. In preparation for this assay, DITHP is expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector containing DITHP cDNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of DITHP. Extracts containing solubilized proteins can be prepared from cells expressing DITHP by methods well known in the art. Portions of the extract containing DITHP are added to [³²P]-labeled RNA or DNA. Radioactive nucleic acid can be synthesized in vitro by techniques well known in the art. The mixtures are incubated at 25° C. in the presence of RNase- and DNase-inhibitors under buffered conditions for 5-10 minutes. After incubation, the samples are analyzed by polyacrylamide gel electrophoresis followed by autoradiography. The presence of a band on the autoradiogram indicates the formation of a complex between DITHP and the radioactive transcript. A band of similar mobility will not be present in samples prepared using control extracts prepared from untransformed cells.

[0855] In the alternative, a method to determine the methylase activity of a DITHP measures transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate. Reaction mixtures (50 μl final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl₂, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [methyl-³H]AdoMet (0.375 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, and acceptor substrate (e.g., 0.4 μg [³⁵S]RNA, or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30° C. for 30 minutes, then 65° C. for 5 minutes. Analysis of [methyl-³H]RNA is as follows: 1) 50 μl of 2× loading buffer (20 mM Tris-HCl, pH 7.6, 1 M LiCl, 1 mM EDTA, 1% sodium dodecyl sulphate (SDS)) and 50 μl oligo d(T)-cellulose (10 mg/ml in 1× loading buffer) are added to the reaction mixture, and incubated at ambient temperature with shaking for 30 minutes. 2) Reaction mixtures are transferred to a 96-well filtration plate attached to a vacuum apparatus. 3) Each sample is washed sequentially with three 2.4 ml aliquots of 1× oligo d(T) loading buffer containing 0.5% SDS, 0.1% SDS, or no SDS. and 4) RNA is eluted with 300 μl of water into a 96-well collection plate, transferred to scintillation vials containing liquid scintillant, and radioactivity determined. Analysis of [methyl-³H]6-MP is as follows: 1) 500 μl 0.5 M borate buffer, pH 10.0, and then 2.5 ml of 20% (v/v) isoamyl alcohol in toluene are added to the reaction mixtures. 2) The samples mixed by vigorous vortexing for ten seconds. 3) After centrifugation at 700 g for 10 minutes, 1.5 ml of the organic phase is transferred to scintillation vials containing 0.5 ml absolute ethanol and liquid scintillant, and radioactivity determined. and 4) Results are corrected for the extraction of 6-MP into the organic phase (approximately 41%).

[0856] An assay for adhesion activity of DITHP measures the disruption of cytoskeletal filament networks upon overexpression of DITHP in cultured cell lines (Rezniczek, G. A. et al. (1998) J. Cell Biol. 141:209-225). cDNA encoding DITHP is subcloned into a mammalian expression vector that drives high levels of cDNA expression. This construct is transfected into cultured cells, such as rat kangaroo PtK2 or rat bladder carcinoma 804G cells. Actin filaments and intermediate filaments such as keratin and vimentin are visualized by immunofluorescence microscopy using antibodies and techniques well known in the art. The configuration and abundance of cytoskeletal filaments can be assessed and quantified using confocal imaging techniques. In particular, the bundling and collapse of cytoskeletal filament networks is indicative of DITHP adhesion activity.

[0857] Alternatively, an assay for DITHP activity measures the expression of DITHP on the cell surface. cDNA encoding DITHP is transfected into a non-leukocytic cell line. Cell surface proteins are labeled with biotin (de la Fuente, M. A. et al. (1997) Blood 90:2398-2405). Immunoprecipitations are performed using DITHP-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled immunoprecipitant is proportional to the amount of DITHP expressed on the cell surface.

[0858] Alternatively, an assay for DITHP activity measures the amount of cell aggregation induced by overexpression of DITHP. In this assay, cultured cells such as NIH3T3 are transfected with cDNA encoding DITHP contained within a suitable mammalian expression vector under control of a strong promoter. Cotransfection with cDNA encoding a fluorescent marker protein, such as Green Fluorescent Protein (CLONTECH), is useful for identifying stable transfectants. The amount of cell agglutination, or clumping, associated with transfected cells is compared with that associated with untransfected cells. The amount of cell agglutination is a direct measure of DITHP activity.

[0859] DITHP may recognize and precipitate antigen from serum. This activity can be measured by the quantitative precipitin reaction (Golub, E. S. et al. (1987) Immunology: A Synthesis, Sinauer Associates, Sunderland Mass., pages 113-115). DITHP is isotopically labeled using methods known in the art. Various serum concentrations are added to constant amounts of labeled DITHP. DITHP-antigen complexes precipitate out of solution and are collected by centrifugation. The amount of precipitable DITHP-antigen complex is proportional to the amount of radioisotope detected in the precipitate. The amount of precipitable DITHP-antigen complex is plotted against the serum concentration. For various serum concentrations, a characteristic precipitation curve is obtained, in which the amount of precipitable DITHP-antigen complex initially increases proportionately with increasing serum concentration, peaks at the equivalence point, and then decreases proportionately with further increases in serum concentration. Thus, the amount of precipitable DITHP-antigen complex is a measure of DITHP activity which is characterized by sensitivity to both limiting and excess quantities of antigen.

[0860] A microtubule motility assay for DITHP measures motor protein activity. In this assay, recombinant DITHP is immobilized onto a glass slide or similar substrate. Taxol-stabilized bovine brain microtubules (commercially available) in a solution containing ATP and cytosolic extract are perfused onto the slide. Movement of microtubules as driven by DITHP motor activity can be visualized and quantified using video-enhanced light microscopy and image analysis techniques. DITHP motor protein activity is directly proportional to the frequency and velocity of microtubule movement.

[0861] Alternatively, an assay for DITHP measures the formation of protein filaments in vitro. A solution of DITHP at a concentration greater than the “critical concentration” for polymer assembly is applied to carbon-coated grids. Appropriate nucleation sites may be supplied in the solution. The grids are negative stained with 0.7% (w/v) aqueous uranyl acetate and examined by electron microscopy. The appearance of filaments of approximately 25 nm (microtubules), 8 nm (actin), or 10 nm (intermediate filaments) is a demonstration of protein activity.

[0862] DITHP electron transfer activity is demonstrated-by oxidation or reduction of NADP. Substrates such as Asn-βGal, biocytidine, or ubiquinone-10 may be used. The reaction mixture contains 1-2 mg/ml HORP, 15 mM substrate, and 2.4 mM NAD(P)⁺ in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na₂HPO₄ buffer, pH 7.4 (reduction reaction); in a total volume of 0.1 ml. FAD may be included with NAD, according to methods well known in the art. Changes in absorbance are measured using a recording spectrophotometer. The amount of NAD(P)H is stoichiometrically equivalent to the amount of substrate initially present, and the change in A₃₄₀ is a direct measure of the amount of NAD(P)H produced; ΔA₃₄₀ =6620[NADH]. DITHP activity is proportional to the amount of NAD(P)H present in the assay. The increase in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858).

[0863] DITHP transcription factor activity is measured by its ability to stimulate transcription of a reporter gene (Liu, H. Y. et al. (1997) EMBO J. 16:5289-5298). The assay entails the use of a well characterized reporter gene construct, LexA_(op)-LacZ, that consists of LexA DNA transcriptional control elements (LexA_(op)) fused to sequences encoding the E. coli LacZ enzyme. The methods for constructing and expressing fusion genes, introducing them into cells, and measuring LacZ enzyme activity, are well known to those skilled in the art. Sequences encoding DITHP are cloned into a plasmid that directs the synthesis of a fusion protein, LexA-DITHP, consisting of DITHP and a DNA binding domain derived from the LexA transcription factor. The resulting plasmid, encoding a LexA-DITHP fusion protein, is introduced into yeast cells along with a plasmid containing the LexA_(op)-LacZ reporter gene. The amount of LacZ enzyme activity associated with LexA-DITHP transfected cells, relative to control cells, is proportional to the amount of transcription stimulated by the DITHP.

[0864] Chromatin activity of DITHP is demonstrated by measuring sensitivity to DNase I (Dawson, B. A. et al. (1989) J. Biol. Chem. 264:12830-12837). Samples are treated with DNase I, followed by insertion of a cleavable biotinylated nucleotide analog, 5-[(N-biotinamido)hexanoamido-ethyl-1,3-thiopropionyl-3-aminoallyl]-2′-deoxyuridine 5′-triphosphate using nick-repair techniques well known to those skilled in the art. Following purification and digestion with EcoRI restriction endonuclease, biotinylated sequences are affinity isolated by sequential binding to streptavidin and biotincellulose.

[0865] Another specific assay demonstrates the ion conductance capacity of DITHP using an electrophysiological assay. DITHP is expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector encoding DITHP. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. A small amount of a second plasmid, which expresses any one of a number of marker genes such as β-galactosidase, is co-transformed into the cells in order to allow rapid identification of those cells which have taken up and expressed the foreign DNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of DITHP and β-galactosidase. Transformed cells expressing β-galactosidase are stained blue when a suitable colorimetric substrate is added to the culture media under conditions that are well known in the art. Stained cells are tested for differences in membrane conductance due to various ions by electrophysiological techniques that are well known in the art. Untransformed cells, and/or cells transformed with either vector sequences alone or β-galactosidase sequences alone, are used as controls and tested in parallel. The contribution of DITHP to cation or anion conductance can be shown by incubating the cells using antibodies specific for either DITHP. The respective antibodies will bind to the extracellular side of DITHP, thereby blocking the pore in the ion channel, and the associated conductance.

[0866] XV. Functional Assays

[0867] DITHP function is assessed by expressing dithp at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Corporation, Carlsbad Calif.), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-transfected.

[0868] Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties.

[0869] FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York N.Y.

[0870] The influence of DITHP on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding DITHP and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success N.Y.). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding DITHP and other genes of interest can be analyzed by northern analysis or microarray techniques.

[0871] XVI. Production of Antibodies

[0872] DITHP substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M. G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.

[0873] Alternatively, the DITHP amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel, 1995, supra, Chapter 11.)

[0874] Typically, peptides 15 residues in length are synthesized using an ABI 431A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, supra.) Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.

[0875] XVII. Purification of Naturally Occurring DITHP Using Specific Antibodies

[0876] Naturally occurring or recombinant DITHP is substantially purified by immunoaffinity chromatography using antibodies specific for DITHP. An immunoaffinity column is constructed by covalently coupling anti-DITHP antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

[0877] Media containing DITHP are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of DITHP (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/DITHP binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and DITHP is collected.

[0878] XVIII. Identification of Molecules Which Interact with DITHP

[0879] DITHP, or biologically active fragments thereof, are labeled with ¹²⁵I Bolton-Hunter reagent. (See, e.g., Bolton, A. E. and W. M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled DITHP, washed, and any wells with labeled DITHP complex are assayed. Data obtained using different concentrations of DITHP are used to calculate values for the number, affinity, and association of DITHP with the candidate molecules.

[0880] Alternatively, molecules interacting with DITHP are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH).

[0881] DITHP may also be used in the PATHCALLING process (CuraGen Corp., New Haven Conn.) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U.S. Pat. No. 6,057,101).

[0882] All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims. TABLE 1 SEQ Probability ID NO: Template ID GI Number Score Annotation 1 061149.1.j g3073775 3.20E−31 heparan-sulfate 6-sulfotransferase 2 404508.3.j g55535 1.30E−35 100 kDa protein 3 441227.2.j g2896147 0 Human alpha-methylacyl-CoA racemase mRNA, complete cds. 4 277927.2 g2708639 2.80E−49 carbonic anhydrase precursor 5 475311.1 g6815284 0 Homo sapiens methionine adenosyltransferase regulatory beta subunit mRNA, complete cds. 6 13039.2 g35790 1.70E−12 protein-tyrosine phosphatase 7 238005.4 g4321619 9.40E−96 seven transmembrane domain orphan receptor 8 345322.1.j g206352 1.50E−15 protein phosphatase inhibitor-1 protein 9 348094.6.j g3876117 3.80E−77 similarity to mouse nek1 protein kinase 10 233678.1 g6179911 0 Homo sapiens ADP-ribosylation factor binding protein GGA1 (GGA1) mRNA, complete cds. 11 312243.1 g3925265 6.90E−21 similar to Probable rabGAP domains 12 425487.3 g6179913 1.00E−154 Homo sapiens ADP-ribosylation factor binding protein GGA2 (GGA2) mRNA, complete cds. 13 346813.3.j g2088550 0 Human hereditary haemochromatosis region, histone 2A-like protein gene, hereditary haemochromatosis (HLA-H) gene, RoRet gene, and sodium phosphate transporter (NPT3) gene, complete cds. 14 006861.1.j g1263080 4.00E−52 Human mariner1 transposase gene, complete consensus sequence. 15 028008.3.j g2463648 5.00E−37 snRNP core Sm protein homolog Sm-X5 16 346078.5.j g3746839 0 Human 45 kDa splicing factor mRNA, complete cds. 17 394637.1.j g1263080 0 Human mariner1 transposase gene, complete consensus sequence. 18 222429.3 g337451 1.90E−17 hnRNP type A/B protein 19 366739.2 g5524926 0 Homo sapiens mRNA for deoxyribonuclease III (drn3 gene). 20 474635.6 g3880433 4.90E−16 similar to mitochondrial RNA splicing MSR4 like protein; cDNA EST EMBL: C09217 comes from this gene 21 228470.1.j g514373 1.00E−80 Opioid-binding cell adhesion molecule 22 407090.5.j g500858 1.20E−10 50 kDa lectin 23 068194.1.j g397947 1.40E−23 thioredoxin 24 411449.2 g5295993 0 Homo sapiens SDHD gene for small subunit of cytochrome b of succinate dehydrogenase, complete cds. 25 18549.2 g4455608 1.50E−20 dJ742C19.2 (APOBEC1 (Apolipoprotein B mRNA editing protein) and Phorbolin 1 LIKE) 26 236043.3 g562263 1.20E−94 tropomodulin 27 445433.2 g28251 6.00E−25 Human mRNA for beta-actin. 28 344630.7.j g40828 5.40E−30 Hyd gamma (homologous to the periplasmic hydrogenase) 29 257121.2 g550123 2.30E−163 GEG-154 30 243794.1.j g36131 0 Human mRNA for ribosomal protein L32. 31 442085.1.j g437878 4.50E−25 ribosomal protein S24 32 370661.3.j g1016712 1.40E−28 Fos-related antigen 33 427939.17.j g488555 1.20E−85 zinc finger protein ZNF135 34 430569.2.j g487784 9.00E−16 Human zinc finger protein ZNF136. 35 444689.1.j g487784 1.00E−26 Human zinc finger protein ZNF136. 36 445198.1.j g498152 3.70E−35 ha0946 protein is Kruppel-related 37 84399.1 g207696 2.80E−17 zinc finger protein 38 350044.1 g1613847 5.00E−10 Human zinc finger protein zfp6 (ZF6) mRNA, partial cds. 39 441329.2 g3006231 4.10E−78 Zn-finger-like protein; similar to Z98745 (PID: g2924250) 40 442401.2 g498722 4.00E−62 Human HZF2 mRNA for zinc finger protein. 41 444933.2 g456269 1.80E−20 zinc finger protein 30 42 481129.4 g3876716 3.10E−15 similar to Zinc finger, C3HC4 type (RING finger) 43 481999.1 g4519269 3.00E−45 Human ZK1 mRNA for Kruppel-type zinc finger protein, complete cds. 44 233814.1.j g1326367 7.50E−11 Similar to the mitochondrial carrier family 45 351376.4.j g517226 7.40E−15 mitochondrial ATPase inhibitor 46 338992.1 g414797 2.80E−253 pyruvate dehydrogenase phosphatase 47 200587.3.j g722379 7.50E−23 similar to NIFS protein (nitrogen fixation) 48 246727.5.j g337456 4.00E−25 Human ribonucleoprotein (La) mRNA, 3′ end. 49 407087.3.j g1176422 7.40E−72 rhophilin 50 441779.1.j g1304381 8.10E−56 hemoglobin alpha chain 51 206603.1 g4101720 4.00E−14 lymphocyte specific formin related protein 52 435694.2 g4572570 3.00E−22 Homo sapiens Jun dimerization protein gene, partial cds; cfos gene, complete cds; and unknown gene.

[0883] TABLE 2 SEQ ID NO: Template ID Start Stop Frame Pfam Hit Pfam Description E-value 6 13039.2 568 801 forward 1 fn3 Fibronectin type III domain 3.00E−09 9 348094.6.j 255 779 forward 3 pkinase Eukaryotic protein kinase 1.10E−53 domain 9 348094.6.j 782 967 forward 2 pkinase Eukaryotic protein kinase 2.70E−08 domain 10 233678.1 149 514 forward 2 VHS VHS domain 1.30E−06 11 312243.1 703 1263 forward 1 TBC TBC domain 2.20E−07 12 42587.3 78 407 forward 3 VHS VHS domain 2.90E−09 16 346078.5.j 844 978 forward 1 G-patch G-patch domain 8.00E−08 20 474635.6 258 530 forward 3 mito_carr Mitochondrial carrier proteins 4.10E−17 20 474635.6 2449 2652 forward 1 mito_carr Mirochondrial carrier proteins 2.40E−10 21 228470.1.j 312 515 forward 3 ig Immunoglobulin domain 6.20E−08 29 257121.2 344 541 forward 2 IBR IBR domain 7.70E−23 30 243794.1.j 456 740 forward 3 Ribosomal_L32e Ribosomal protein L32 8.00E−20 30 243794.1.j 231 326 forward 3 Ribosomal_S14 Ribosomal protein S14p/S29e 1.40E−12 31 442085.1.j 149 400 forward 2 Ribosomal_S24e Ribosomal protein S24e 4.70E−40 33 427939.17.j 1002 1070 forward 3 zf-C2H2 Zinc finger, C2H2 type 1.70E−07 33 427939.17.j 589 657 forward 1 zf-C2H2 Zinc finger, C2H2 type 4.80E−07 35 444689.1.j 170 274 forward 2 KRAB KRAB box 8.70E−06 36 445198.1.j 80 268 forward 2 KRAB KRAB box 2.90E−42 38 350044.1 76 240 forward 1 KRAB KRAB box 4.40E−12 38 350044.1 895 963 forward 1 zf-C2H2 Zinc finger, C2H2 type 8.40E−06 39 441329.2 684 965 forward 3 SCAN SCAN domain 5.30E−48 40 442401.2 206 394 forward 2 KRAB KRAB box 2.40E−41 41 444933.2 292 480 forward 1 KRAB KRAB box 1.40E−41 43 481999.1 371 547 forward 2 KRAB KRAB box 1.90E−15 43 481999.1 839 907 forward 2 zf-C2H2 Zinc finger, C2H2 type 1.40E−04 44 233814.1.j 356 625 forward 2 mito_carr Mitochondrial carrier proteins 2.10E−19 46 338992.1 1156 1680 forward 1 PP2C Protein phosphatase 2C 1.90E−54 46 338992.1 840 1184 forward 3 PP2C Protein phosphatase 2C 3.30E−10 47 200587.3.j 146 1276 forward 2 aminotran_5 Aminotransferases class-V 3.20E−32 50 441779.1.j 76 498 forward 1 globin Globin 4.20E−53

[0884] TABLE 3 SEQ ID NO: Template ID Start Stop Frame Domain Type 2 404508.3.j 468 548 reverse 3 TM 2 404508.3.j 549 626 forward 3 SP 2 404058.3.j 348 428 reverse 3 TM 2 404508.3.j 430 513 reverse 1 SP 2 404508.3.j 459 539 forward 3 TM 3 441227.2.j 523 606 forward 1 SP 6 13039.2 1507 1581 forward 1 TM 7 238005.4 887 973 forward 2 SP 7 238005.4 1691 1783 forward 2 SP 7 238005.4 1583 1678 forward 2 SP 7 238005.4 566 643 forward 2 TM 9 348094.6.j 1994 2077 forward 2 TM 9 348094.6.j 1871 1948 reverse 2 TM 9 348094.6.j 2046 2117 forward 3 TM 9 348094.6.j 2112 2195 reverse 3 TM 9 348094.6.j 2035 2115 forward 1 TM 9 348094.6.j 2920 3000 forward 1 TM 10 233678.1 2412 2495 forward 3 SP 11 312243.1 528 614 forward 3 SP 16 346078.5.j 1406 1492 forward 2 TM 17 394637.1.j 36 122 forward 3 TM 18 222429.3 646 726 forward 1 SP 19 366739.2 791 880 forward 2 SP 19 366739.2 1115 1207 forward 2 SP 20 474635.6 1293 1370 forward 3 TM 22 407090.5.j 2955 3038 reverse 3 SP 24 411449.2 283 366 forward 1 SP 27 445433.2 123 203 forward 3 TM 29 257121.2 3656 3736 forward 2 TM 29 257121.2 851 934 forward 2 TM 46 338992.1 1601 1690 forward 2 SP 46 338992.1 1478 1561 forward 2 SP

[0885] TABLE 4 SEQ ID NO: Template ID Component ID Start Stop 4 277927.2 g1623387 349 631 4 277927.2 g1626390 361 610 4 277927.2 6064353H1 565 854 4 277927.2 g1615271 681 1040 4 277927.2 5107163H1 730 966 4 277927.2 5107163F6 730 1186 4 277927.2 4317715H1 771 1044 4 277927.2 4317712H1 771 1042 4 277927.2 382292H1 773 1051 4 277927.2 3877607H1 943 1226 4 277927.2 1742979R6 1092 1596 4 277927.2 1742979T6 1092 1636 4 277927.2 1742979H1 1092 1368 4 277927.2 g1441482 1103 1496 4 277927.2 989077H1 1106 1348 4 277927.2 g2080036 1107 1623 4 277927.2 2706884T6 1116 1639 4 277927.2 g1156807 1156 1455 4 277927.2 g759629 1182 1464 4 277927.2 g1013585 1183 1541 4 277927.2 494376T7 1192 1625 4 277927.2 3959505H2 286 570 4 277927.2 g1060652 296 603 4 277927.2 g2079874 1189 1681 4 277927.2 4317170T6 1193 1651 4 277927.2 g2703976 1208 1684 4 277927.2 5107163T6 1217 1645 4 277927.2 g3701929 1217 1679 4 277927.2 995158H1 1218 1362 4 277927.2 g1118374 1232 1680 4 277927.2 g2524334 1232 1680 4 277927.2 494376T6 1251 1625 4 277927.2 g2675274 1288 1641 4 277927.2 g1991480 1302 1585 4 277927.2 2720938H1 1308 1551 4 277927.2 g1062338 1315 1658 4 277927.2 g1474145 1321 1683 4 277927.2 g1803519 1339 1682 4 277927.2 g1157288 1346 1680 4 277927.2 g1219901 1370 1681 4 277927.2 2603851T6 1382 1630 4 277927.2 g1123763 1399 1680 4 277927.2 g1013586 1406 1682 4 277927.2 g1012521 1429 1680 4 277927.2 836696H1 1468 1669 4 277927.2 g3230141 1515 1680 4 277927.2 g759576 1517 1676 4 277927.2 g1225498 1532 1704 4 277927.2 g1140899 1604 1680 4 277927.2 4317170H1 1 199 4 277927.2 2706884H1 1 199 4 277927.2 4317170F6 1 384 4 277927.2 2706884F6 1 320 4 277927.2 g1062337 36 388 4 277927.2 g1064195 39 230 4 277927.2 2862653H1 42 117 4 277927.2 494376H1 53 305 4 277927.2 494376R7 53 383 4 277927.2 494376R6 53 492 4 277927.2 g1275473 57 586 4 277927.2 g2055898 59 543 4 277927.2 2707487H1 64 162 4 277927.2 491071H1 74 319 4 277927.2 g1975146 80 403 4 277927.2 g1142488 84 471 4 277927.2 g1839772 84 214 4 277927.2 g1012520 84 292 4 277927.2 3396290H1 86 344 4 277927.2 5896091H1 246 523 4 277927.2 g946240 246 551 4 271927.2 g943428 247 449 5 475311.1 1948746H1 1 233 5 475311.1 g614088 12 271 5 475311.1 5644994H1 32 287 5 475311.1 g645077 37 260 5 475311.1 g668814 40 366 5 475311.1 g645713 42 263 5 475311.1 g645045 42 359 5 475311.1 4297187H1 46 315 5 475311.1 3486028H1 53 385 5 475311.1 g683448 54 438 5 475311.1 g645139 54 252 5 475311.1 g645138 54 316 5 475311.1 g670408 54 433 5 475311.1 g646240 56 444 5 475311.1 g562499 56 444 5 475311.1 g4113162 56 511 5 475311.1 g2003099 59 473 5 475311.1 g815985 71 481 5 475311.1 g674342 77 421 5 475311.1 4151149H1 88 355 5 475311.1 3843963H1 88 393 5 475311.1 5029373H1 92 346 5 475311.1 3584334H1 98 435 5 475311.1 g3015753 105 441 5 475311.1 g831378 105 457 5 475311.1 g900504 105 401 5 475311.1 g817737 105 402 5 475311.1 g817003 105 418 5 475311.1 g812268 105 397 5 475311.1 g2052991 105 462 5 475311.1 g3922575 105 509 5 475311.1 g2884797 105 548 5 475311.1 g2354824 105 375 5 475311.1 g2788503 105 214 5 475311.1 g797560 105 342 5 475311.1 g820611 105 346 5 475311.1 g821223 105 347 5 475311.1 g1678742 138 543 5 475311.1 5590296H1 150 396 5 475311.1 2446939H1 155 407 5 475311.1 4178404H1 164 434 5 475311.1 4970343H1 179 455 5 475311.1 g1720508 218 502 5 475311.1 4816085H1 242 326 5 475311.1 g1296172 248 789 5 475311.1 5778021H1 256 544 5 475311.1 1579546F6 263 712 5 475311.1 1227469H1 263 535 5 475311.1 1951396H1 287 527 5 475311.1 g1980791 307 631 5 475311.1 3369048H1 322 455 5 475311.1 261669H1 325 559 5 475311.1 1005556H1 344 651 5 475311.1 g1987083 364 686 5 475311.1 3153327H1 364 683 5 475311.1 5086472H1 372 552 5 475311.1 g2038507 365 782 5 475311.1 3791124H1 366 623 5 475311.1 3342191H1 383 665 5 475311.1 2727001H1 403 658 5 475311.1 5691335H1 421 697 5 475311.1 2246168H1 434 702 5 475311.1 4186012H1 582 933 5 475311.1 2630947H1 653 899 5 475311.1 g1444007 793 1005 6 13039.2 4189083H1 3573 3883 6 13039.2 g3802900 3582 3888 6 13039.2 2881380H1 3588 3897 6 13039.2 g864431 3590 3852 6 13039.2 g1481926 3594 3881 6 13039.2 g667472 3600 3883 6 13039.2 g3154327 3607 3891 6 13039.2 4583956H1 3611 3880 6 13039.2 g776778 3615 3887 6 13039.2 2381092H1 3622 3854 6 13039.2 3810284H1 3623 3895 6 13039.2 4906362H2 3624 3904 6 13039.2 2202368H1 3632 3875 6 13039.2 g4072852 3636 4070 6 13039.2 2561132H1 3646 3748 6 13039.2 1294323F1 3648 3884 6 13039.2 1294323H1 3648 3780 6 13039.2 446234H1 3649 3871 6 13039.2 4774923H1 3650 3935 6 13039.2 g789650 3651 3882 6 13039.2 g1220073 3652 3888 6 13039.2 g776622 3658 3886 6 13039.2 g1522080 3663 3883 6 13039.2 449477H1 3667 3875 6 13039.2 2293709H1 3669 3884 6 13039.2 g1114992 3695 3885 6 13039.2 g667182 3700 3883 6 13039.2 g1162269 3703 4063 6 13039.2 g1773892 3703 4081 6 13039.2 g3887238 3705 4083 6 13039.2 3542520H1 3707 3870 6 13039.2 4633040H1 3727 4003 6 13039.2 g1128515 3763 4081 6 13039.2 2804481H1 3793 3899 6 13039.2 556467R6 3816 3871 6 13039.2 556467H1 3816 3871 6 13039.2 g683155 3819 4075 6 13039.2 g878104 3824 4075 6 13039.2 2945643H1 3841 4076 6 13039.2 g821501 3869 4087 6 13039.2 g782508 3869 4083 6 13039.2 2590326H2 4016 4075 6 13039.2 4535971T6 1081 1596 6 13039.2 2887511H1 1137 1386 6 13039.2 5060591H1 1078 1278 6 13039.2 2261086H1 1154 1385 6 13039.2 3535673H1 1214 1493 6 13039.2 1951291H1 1264 1453 6 13039.2 488798H1 1330 1587 6 13039.2 2634402H1 1381 1594 6 13039.2 2135368H1 1421 1684 6 13039.2 2135368F6 1421 1863 6 13039.2 2837860T6 3920 4029 6 13039.2 2837860F6 3927 4069 6 13039.2 2837860H1 3927 4069 6 13039.2 3536266H1 3936 4027 6 13039.2 3536268H1 3937 4038 6 13039.2 g776777 3055 3279 6 13039.2 g1856268 3100 3505 6 13039.2 2604507H1 3110 3384 6 13039.2 5065865H1 3071 3344 6 13039.2 3472443H1 3077 3330 6 13039.2 5017370H1 3114 3384 6 13039.2 2767212H1 3090 3334 6 13039.2 790129R1 3121 3597 6 13039.2 2690375H1 3094 3357 6 13039.2 2411049H1 3099 3334 6 13039.2 g1976982 1594 1956 6 13039.2 2642416H1 1599 1728 6 13039.2 g1476955 1606 2005 6 13039.2 g1062967 1606 1901 6 13039.2 g1481925 1606 1784 6 13039.2 3136852H1 1738 2037 6 13039.2 2500241H1 1778 2029 6 13039.2 2788782H1 1863 2121 6 13039.2 874642H1 1862 2024 6 13039.2 g1200951 1869 2062 6 13039.2 4535987H1 1879 2008 6 13039.2 4536041H1 1884 2151 6 13039.2 1921318T6 3558 4028 6 13039.2 g2458968 3562 3880 6 13039.2 3434402H1 1 237 6 13039.2 g1774870 25 371 6 13039.2 5090377H1 28 270 6 13039.2 5090377F6 28 341 6 13039.2 g2243533 71 456 6 13039.2 4535971H1 377 641 6 13039.2 4535971F6 377 900 6 13039.2 2738090H1 634 871 6 13039.2 2738090F6 634 1152 6 13039.2 4032617H1 652 788 6 13039.2 3247382H1 687 986 6 13039.2 2886124H1 2974 3263 6 13039.2 2886134H1 2974 3255 6 13039.2 2882975H1 2974 3267 6 13039.2 731806R1 2984 3499 6 13039.2 3715202H1 2984 3092 6 13039.2 g1993687 2985 3312 6 13039.2 731806H1 2984 3258 6 13039.2 2468144H1 2990 3229 6 13039.2 1907815H1 2991 3218 6 13039.2 4148570H1 3006 3269 6 13039.2 g778804 3015 3330 6 13039.2 3256396H1 3017 3269 6 13039.2 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3849 29 257121.2 g2278678 3527 3855 29 257121.2 g2595803 3528 3819 29 257121.2 g1994549 3533 3860 29 257121.2 g613905 3177 3513 29 257121.2 5905841H1 3186 3500 29 257121.2 1444396H1 3186 3461 29 257121.2 g4187265 3195 3670 29 257121.2 2473816T6 3190 3808 29 257121.2 g4186245 3195 3664 29 257121.2 g3278632 3196 3616 29 257121.2 g1506304 3213 3436 29 257121.2 1658291H1 3211 3453 29 257121.2 g1994550 2249 2499 29 257121.2 3053733H1 2279 2581 29 257121.2 5641114H1 2298 2545 29 257121.2 995725R1 2300 2819 29 257121.2 995725H1 2300 2596 29 257121.2 2173193F6 2302 2653 29 257121.2 2173193H1 2302 2536 29 257121.2 3474978H1 2324 2601 29 257121.2 2106564H1 2329 2585 29 257121.2 5171463H1 2343 2629 29 257121.2 3449591H1 2355 2601 29 257121.2 2824470T6 2356 2941 29 257121.2 5546639H1 2387 2525 29 257121.2 5658068H1 2396 2642 29 257121.2 3771054H1 1386 1692 29 257121.2 2714558T6 1407 1749 29 257121.2 g2037431 1419 1693 29 257121.2 2436316H1 1459 1650 29 257121.2 g953893 1502 1633 29 257121.2 6075654H1 1487 1796 29 257121.2 g1055687 1504 1601 29 257121.2 g2034372 1557 1818 29 257121.2 1235661H1 1567 1836 29 257121.2 2824470F6 1573 1997 29 257121.2 2824470H1 1573 1809 29 257121.2 g4509712 1585 1995 29 257121.2 g3700825 1587 1927 29 257121.2 4876427H1 1618 1807 29 257121.2 3297894H1 1657 1904 29 257121.2 g3764184 1663 1795 29 257121.2 4306167H1 1689 1809 29 257121.2 446319T6 1703 2175 29 257121.2 5984668H1 1802 2091 29 257121.2 5594456H1 1805 1931 29 257121.2 3202943H1 1818 2073 29 257121.2 309745H1 3396 3648 29 257121.2 4652103H1 3402 3556 29 257121.2 g3058761 3407 3849 29 257121.2 g3961167 3409 3844 29 257121.2 g3178632 3413 3849 29 257121.2 5645258H1 190 462 29 257121.2 g751765 209 449 29 257121.2 g751766 344 636 29 257121.2 2478708H1 363 607 29 257121.2 5544313H1 370 582 29 257121.2 1911275H1 460 725 29 257121.2 1437425F1 511 985 29 257121.2 1437426H1 511 734 29 257121.2 1437425H1 511 736 29 257121.2 3697654H1 541 823 29 257121.2 3333937H1 589 769 29 257121.2 2639996H1 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3672 3830 29 257121.2 3729288H1 3676 3853 29 257121.2 g1813011 3677 3855 29 257121.2 g2063050 3680 3849 29 257121.2 3729209T1 3681 3810 29 257121.2 g2063735 3707 3849 29 257121.2 g2882056 3741 3849 29 257121.2 1547677H1 3769 3844 29 257121.2 6024576H1 2558 2843 29 257121.2 4909221H1 2607 2901 29 257121.2 1427954H1 2634 2884 29 257121.2 5170995H1 2648 2874 29 257121.2 1427954F6 2665 3120 29 257121.2 946401H1 2666 2926 29 257121.2 1374579H1 2670 2923 29 257121.2 2261955H1 2684 2948 29 257121.2 3094766H1 2691 2994 29 257121.2 2741005H1 2693 2978 29 257121.2 4635067H1 2704 2978 29 257121.2 1007503H1 2718 3048 29 257121.2 5284328H1 2720 2957 29 257121.2 5064384H1 2731 2941 29 257121.2 1672059H1 2742 2924 29 257121.2 1672008H1 2742 2975 29 257121.2 1672059F6 2742 3123 29 257121.2 2410045H1 2774 3011 37 84399.1 2520472H1 1 226 37 84399.1 g4148125 155 499 38 350044.1 3110061F7 1 276 38 350044.1 3110061H1 3 289 38 350044.1 4308349H1 158 426 38 350044.1 4308349F6 158 587 38 350044.1 5333549H1 185 413 38 350044.1 3399811H1 405 650 38 350044.1 2288313H1 496 629 38 350044.1 4637040H1 583 844 38 350044.1 4637040F6 582 916 38 350044.1 4308349T6 662 1020 38 350044.1 308559H1 664 884 38 350044.1 g1803082 832 926 38 350044.1 3977826H1 852 968 39 441329.2 g3751157 1 412 39 441329.2 g1470664 342 578 39 441329.2 g1395945 342 644 39 441329.2 4327736H1 355 622 39 441329.2 132848H1 360 540 39 441329.2 132849R6 360 805 39 441329.2 131890H1 360 563 39 441329.2 131890R6 360 802 39 441329.2 g1165579 361 542 39 441329.2 g1928191 371 650 39 441329.2 4204432F6 374 765 39 441329.2 g1734964 378 763 39 441329.2 3357071H1 701 979 39 441329.2 3357071F6 701 1118 39 441329.2 131890T6 1077 1235 39 441329.2 g1733361 1084 1235 39 441329.2 132849T6 1123 1235 39 441329.2 4204432T6 1128 1235 40 442401.2 3349655H1 1 327 40 442401.2 4309840H1 10 304 40 442401.2 4349106H1 25 238 40 442401.2 5043378H1 42 296 40 442401.2 4789236H1 44 123 40 442401.2 5320882H1 45 180 40 442401.2 2551237H1 64 319 40 442401.2 4664370H1 71 322 40 442401.2 3510753H1 75 389 40 442401.2 693783H1 80 286 40 442401.2 693783R6 83 554 40 442401.2 3865603H1 88 388 40 442401.2 2289862H1 86 326 40 442401.2 3681694H1 92 386 40 442401.2 693783T6 128 736 40 442401.2 519767H1 511 741 41 444933.2 3492265H1 7 310 41 444933.2 g1501708 7 263 41 444933.2 3155609H1 7 99 41 444933.2 g1474433 9 386 41 444933.2 3118539H1 9 310 41 444933.2 3295816H1 15 277 41 444933.2 1592931H1 29 229 41 444933.2 1592931F6 29 395 41 444933.2 1592931T6 43 579 41 444933.2 3436778H1 1 229 42 481129.4 999203H1 234 552 42 481129.4 999203T1 234 708 42 481129.4 g3278054 236 751 42 481129.4 3868296H1 240 560 42 481129.4 g4522433 240 752 42 481129.4 3137701H1 240 575 42 481129.4 g3417930 241 746 42 481129.4 3868754H1 240 570 42 481129.4 g4070375 243 752 42 481129.4 715742H1 248 618 42 481129.4 4950629H1 245 592 42 481129.4 g3644668 250 755 42 481129.4 1577433H1 250 516 42 481129.4 g3446453 265 747 42 481129.4 2055077H1 267 589 42 481129.4 g2288119 272 746 42 481129.4 3358220H1 293 617 42 481129.4 g3797800 295 747 42 481129.4 g2113046 296 749 42 481129.4 g2740428 301 747 42 481129.4 g2268545 312 747 42 481129.4 g4087282 314 750 42 481129.4 g2017050 320 622 42 481129.4 g1924476 320 647 42 481129.4 g3735602 323 748 42 481129.4 g4532931 324 747 42 481129.4 g3734942 324 751 42 481129.4 g2737174 325 747 42 481129.4 g3960674 330 751 42 481129.4 g2252043 328 746 42 481129.4 g3330470 342 747 42 481129.4 g3960381 342 755 42 481129.4 g4452123 351 746 42 481129.4 g3678389 352 747 42 481129.4 1632555H1 353 564 42 481129.4 1632539H1 353 571 42 481129.4 4228443H1 353 686 42 481129.4 g3108753 369 749 42 481129.4 g2319165 368 747 42 481129.4 g3755458 374 754 42 481129.4 g4086634 397 747 42 481129.4 g2322475 404 746 42 481129.4 g3750698 406 748 42 481129.4 g2021853 411 746 42 481129.4 3099690H1 423 747 42 481129.4 4125491H1 425 735 42 481129.4 5107680H1 443 746 42 481129.4 1253080F1 454 746 42 481129.4 2741014H1 456 747 42 481129.4 g4086632 472 747 42 481129.4 3381102H1 195 363 42 481129.4 3136744H1 132 344 42 481129.4 2485548H1 37 110 42 481129.4 3238530H1 36 320 42 481129.4 5332434H1 132 262 42 481129.4 1743373H1 37 342 42 481129.4 2398059H1 30 282 42 481129.4 5299970H1 36 291 42 481129.4 4857940H1 132 351 42 481129.4 982689H1 28 284 42 481129.4 1684768H1 34 296 42 481129.4 4901916H1 29 347 42 481129.4 4340959H1 25 317 42 481129.4 1275760H1 195 375 42 481129.4 g1975121 132 336 42 481129.4 534025H1 30 348 42 481129.4 3555252H1 24 317 42 481129.4 1504151H1 30 329 42 481129.4 4652858H1 195 379 42 481129.4 4638612H1 132 320 42 481129.4 4801179H1 30 310 42 481129.4 1970489H1 35 306 42 481129.4 2497883H1 30 272 42 481129.4 2557615H1 132 324 42 481129.4 4079990H1 195 386 42 481129.4 3555091H1 31 350 42 481129.4 g1635875 160 388 42 481129.4 3010470H1 132 368 42 481129.4 g1685660 488 846 42 481129.4 2716085H1 492 747 42 481129.4 g2669356 508 750 42 481129.4 g2035379 508 768 42 481129.4 g4330124 517 749 42 481129.4 g1125228 503 768 42 481129.4 g1237906 515 746 42 481129.4 1253080H1 547 746 42 481129.4 1924052H1 559 747 42 481129.4 1444584H1 557 747 42 481129.4 3089459H1 563 755 42 481129.4 1952233H1 596 746 42 481129.4 g2269237 609 746 42 481129.4 2058183R6 620 747 42 481129.4 2058183H1 620 747 42 481129.4 g3321468 627 746 42 481129.4 g2277314 629 747 42 481129.4 4363320H1 652 742 42 481129.4 g2752791 670 746 42 481129.4 3221190H1 49 104 42 481129.4 529956H1 197 303 42 481129.4 1781280H1 202 315 42 481129.4 586079H1 35 104 42 481129.4 644429H1 37 104 42 481129.4 4713384H1 32 97 42 481129.4 1434389H1 30 104 42 481129.4 2286414H1 30 104 42 481129.4 1648951H1 34 111 42 481129.4 3589355H1 36 111 42 481129.4 1916331H1 195 338 42 481129.4 880829H1 28 97 42 481129.4 2475170H1 195 350 42 481129.4 g1301383 263 352 42 481129.4 4612347H1 169 315 42 481129.4 116571H1 25 83 42 481129.4 g1023181 141 205 42 481129.4 835155H1 37 333 42 481129.4 4153116H1 132 329 42 481129.4 4300976H1 132 343 42 481129.4 962735H1 132 324 42 481129.4 4904613H2 132 339 42 481129.4 4904321H1 195 362 42 481129.4 4130260H1 132 334 42 481129.4 534025F1 1 184 42 481129.4 5165213H2 4 265 42 481129.4 g3085628 1 187 42 481129.4 g2836097 1 184 42 481129.4 g2397633 1 179 42 481129.4 g2669712 1 181 42 481129.4 811971T1 1 191 42 481129.4 811971H1 1 67 42 481129.4 g1578417 1 184 42 481129.4 g3016145 1 253 42 481129.4 g1425361 1 232 42 481129.4 g2237584 1 231 42 481129.4 g4072976 1 234 42 481129.4 g3076557 1 252 42 481129.4 3716227H1 1 125 42 481129.4 g2350483 1 232 42 481129.4 g1289724 1 184 42 481129.4 4830687H1 14 227 42 481129.4 1270745H1 1 82 42 481129.4 g3423624 1 187 42 481129.4 g1685572 1 232 42 481129.4 g2907402 1 79 42 481129.4 g2987865 1 235 42 481129.4 4664951H1 1 115 42 481129.4 g1114304 1 162 42 481129.4 1694416H1 1 78 42 481129.4 g4076242 1 234 42 481129.4 g2806310 1 181 42 481129.4 g3110520 1 231 42 481129.4 g3178699 1 235 42 481129.4 5691870H1 1 56 42 481129.4 g2408708 1 232 42 481129.4 g3070820 1 231 42 481129.4 g1194184 1 183 42 481129.4 g3400227 1 296 42 481129.4 g1080367 1 151 42 481129.4 g2768589 1 231 42 481129.4 g3804766 1 184 42 481129.4 g3190855 1 232 42 481129.4 g1087452 1 267 42 481129.4 4065091H1 1 169 42 481129.4 g2838959 1 236 42 481129.4 3091849H1 1 226 42 481129.4 g2263870 1 183 42 481129.4 g2279285 1 239 42 481129.4 2755370H1 1 184 42 481129.4 2757311H1 1 184 42 481129.4 863475H1 1 192 42 481129.4 g1689421 1 183 42 481129.4 5528923H1 19 211 42 481129.4 g1506021 1 184 42 481129.4 2467514H1 10 261 42 481129.4 2943819H1 15 312 42 481129.4 g1043884 16 196 42 481129.4 4461552H1 5 231 42 481129.4 g1281569 1 531 42 481129.4 g727471 1 234 42 481129.4 4889929H1 29 314 42 481129.4 4985113H1 29 354 42 481129.4 1488272H1 5 319 42 481129.4 2450834F6 6 558 42 481129.4 2450834H1 6 287 42 481129.4 g2027943 7 201 42 481129.4 2394311H2 8 123 42 481129.4 3372442H1 1 258 42 481129.4 g3307272 28 238 42 481129.4 3773060H1 38 366 42 481129.4 4125777H1 10 329 42 481129.4 5159564H1 12 302 42 481129.4 3233460H1 12 297 42 481129.4 5552762H1 12 315 42 481129.4 593632H1 12 123 42 481129.4 4513470H1 13 313 42 481129.4 5115162H1 44 356 42 481129.4 5039159H2 15 286 42 481129.4 2134140H1 15 328 42 481129.4 5943202H1 44 374 42 481129.4 027622R6 17 589 42 481129.4 027622H1 17 197 42 481129.4 3115953H1 46 372 42 481129.4 3489959H1 46 382 42 481129.4 5166761H1 44 322 42 481129.4 3626341H1 18 386 42 481129.4 3645933H1 48 327 42 481129.4 3159541H1 19 348 42 481129.4 2741058H1 52 282 42 481129.4 1475821H1 50 252 42 481129.4 4567661H1 22 350 42 481129.4 3601462H1 22 394 42 481129.4 4595577H1 53 283 42 481129.4 3819717H1 22 426 42 481129.4 4975524H1 22 359 42 481129.4 2084168H1 50 348 42 481129.4 5529123H1 18 212 42 481129.4 5700770H1 52 344 42 481129.4 5701471H1 52 355 42 481129.4 g3134982 45 234 42 481129.4 4979603H1 52 355 42 481129.4 3202264H1 23 321 42 481129.4 4938763H1 16 130 42 481129.4 4202906H1 8 274 42 481129.4 526404H1 22 322 42 481129.4 2665708H1 21 280 42 481129.4 2941705H1 22 327 42 481129.4 g1321143 11 346 42 481129.4 g2021854 22 337 42 481129.4 1833977H1 22 134 42 481129.4 2100632H1 12 285 42 481129.4 3675543H1 12 320 42 481129.4 3186510H1 13 400 42 481129.4 3229333H1 14 321 42 481129.4 4885571H1 19 306 42 481129.4 3074685H1 16 321 42 481129.4 3663968H1 16 329 42 481129.4 g2154555 1 29 42 481129.4 863475R1 1 192 42 481129.4 4230048H1 1 176 42 481129.4 3693558H1 18 328 42 481129.4 g1648658 1 23 42 481129.4 584205H1 18 309 42 481129.4 4227248H1 21 324 42 481129.4 g1043979 28 415 42 481129.4 g2142101 1 24 42 481129.4 4203722H1 22 321 42 481129.4 4174825H1 22 337 42 481129.4 5115519H1 23 321 42 481129.4 3133373H1 25 334 42 481129.4 1275760F6 1 147 42 481129.4 1275760F1 1 76 42 481129.4 2051350H1 27 350 42 481129.4 4341005H1 27 398 42 481129.4 3134845H1 1 260 42 481129.4 3484150H1 1 316 42 481129.4 4584348H1 1 279 42 481129.4 g2004902 1 283 42 481129.4 4374817H1 1 288 42 481129.4 g1967486 1 183 42 481129.4 4147580H1 1 267 42 481129.4 g1425470 1 78 42 481129.4 4276424H1 1 301 42 481129.4 082654H1 15 171 42 481129.4 g3003216 1 306 42 481129.4 g1648659 1 183 42 481129.4 4563261H1 1 255 42 481129.4 4563351H1 12 136 42 481129.4 116571F1 1 233 42 481129.4 g4372584 1 234 42 481129.4 3994691H1 23 288 42 481129.4 g2437312 1 188 42 481129.4 136145F1 1 184 42 481129.4 2768229H1 1 256 42 481129.4 5852546H1 1 272 42 481129.4 5844492H1 6 279 42 481129.4 1727158H1 8 249 42 481129.4 1950091H1 8 264 42 481129.4 3204976H1 10 290 42 481129.4 4554858H1 10 275 42 481129.4 5840991H2 11 303 42 481129.4 5840890H2 11 314 42 481129.4 4559105H1 12 298 42 481129.4 871105H1 12 123 42 481129.4 4998348H1 12 293 42 481129.4 871105R1 12 123 42 481129.4 4770486H1 13 287 42 481129.4 3426271H1 14 295 42 481129.4 3273645H1 14 298 42 481129.4 4502129H1 14 202 42 481129.4 3403224H1 15 221 42 481129.4 1511018H1 15 89 42 481129.4 4502229H1 15 288 42 481129.4 4042436H1 8 283 42 481129.4 3845464H1 10 357 42 481129.4 3720453H1 12 340 42 481129.4 1998071H1 22 123 42 481129.4 5835243H1 22 290 42 481129.4 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g2008330 80 340 42 481129.4 881179T1 30 687 42 481129.4 534025R1 32 572 42 481129.4 871105T1 54 123 42 481129.4 g1956736 64 347 42 481129.4 4800988H1 83 224 42 481129.4 g1685765 83 403 42 481129.4 1230023H1 32 172 42 481129.4 1805729H1 27 189 42 481129.4 1320892H1 38 321 42 481129.4 1599902H1 38 290 42 481129.4 4588734H1 85 374 42 481129.4 g1955622 70 445 42 481129.4 3517903H1 40 255 42 481129.4 136145R1 69 590 42 481129.4 4979660H1 40 354 42 481129.4 1741320H1 42 338 42 481129.4 5117019H1 88 386 42 481129.4 g1924567 88 536 42 481129.4 2343536H1 89 355 42 481129.4 4536803H1 90 398 42 481129.4 g2158823 96 655 42 481129.4 g1958858 97 676 42 481129.4 g828123 93 501 42 481129.4 g3988556 97 621 42 481129.4 g3096874 99 539 42 481129.4 g3178165 107 566 42 481129.4 g4079967 110 541 42 481129.4 465693H1 66 199 42 481129.4 g3003210 111 467 42 481129.4 5265746H1 120 374 42 481129.4 966316H1 118 374 42 481129.4 1458085H1 122 396 42 481129.4 1457484H1 122 305 42 481129.4 2109149H1 122 442 42 481129.4 2109149R6 123 704 42 481129.4 g1243536 77 215 42 481129.4 958148H1 122 431 42 481129.4 5020591T1 124 705 42 481129.4 g1087561 133 459 42 481129.4 g1958920 135 700 42 481129.4 g1147415 139 444 42 481129.4 g3890878 103 203 42 481129.4 2401220H1 144 390 42 481129.4 3223013H1 149 494 42 481129.4 1680890H1 149 361 42 481129.4 g1298313 155 667 42 481129.4 828345H1 143 226 42 481129.4 3441046H1 159 442 42 481129.4 2109149T6 163 707 42 481129.4 2004957H1 176 484 42 481129.4 6063286H1 180 511 42 481129.4 5020591H1 179 501 42 481129.4 2450834T6 182 707 42 481129.4 027622T6 183 830 42 481129.4 5597771H1 189 470 42 481129.4 821831T6 192 705 42 481129.4 821831R1 192 746 42 481129.4 821831R6 192 746 42 481129.4 821831F1 192 757 42 481129.4 g2252207 199 748 42 481129.4 1457484R1 199 746 42 481129.4 g3736470 203 746 42 481129.4 g1295465 204 757 42 481129.4 5185783H1 205 496 42 481129.4 g2115256 211 352 42 481129.4 4085165H1 215 541 42 481129.4 g1577977 221 716 42 481129.4 g3593921 222 750 42 481129.4 g3429019 222 747 42 481129.4 5221813H2 225 517 42 481129.4 5863560H1 232 539 42 481129.4 999208H1 234 544 42 481129.4 999203R1 234 750 42 481129.4 g3649202 235 753 42 481129.4 g2265393 234 751 42 481129.4 4049323H1 235 584 43 481999.1 1255239H1 838 1104 43 481999.1 4913234H1 397 512 43 481999.1 1724376H1 864 932 43 481999.1 1509213H1 819 1012 43 481999.1 1849705H1 281 501 43 481999.1 1509213F6 819 1104 43 481999.1 1476972F6 260 574 43 481999.1 g2195301 866 1104 43 481999.1 g985997 864 941 43 481999.1 880602R1 397 512 43 481999.1 g1980533 1 283 43 481999.1 g2195281 987 1104 43 481999.1 5526658H1 780 991 43 481999.1 880602H1 394 457 43 481999.1 1255206H1 838 1104 43 481999.1 1509479F6 819 1104 43 481999.1 3457008H1 397 481 43 481999.1 3641330H1 723 1014 43 481999.1 4181741H1 717 799 43 481999.1 3384087F6 604 857 43 481999.1 4760678H1 1 286 43 481999.1 1509221H1 819 1006 43 481999.1 1509455H1 819 997 43 481999.1 2603491H1 880 1104 43 481999.1 170070H1 797 982 43 481999.1 3427420F6 521 604 43 481999.1 4760678F6 1 499 43 481999.1 4913234F6 235 670 43 481999.1 4072789H1 237 499 43 481999.1 1524891F6 269 890 43 481999.1 398973R1 305 830 43 481999.1 4972169H1 420 695 43 481999.1 4357304H1 435 710 43 481999.1 4181741F6 718 1107 43 481999.1 3123901F6 380 434 43 481999.1 5585642H1 650 868 43 481999.1 1724376F6 864 941 43 481999.1 2938884H1 864 941 43 481999.1 3369038H1 429 706 43 481999.1 g1148977 1 387 43 481999.1 g1971119 842 1104 43 481999.1 g1761297 704 1005 43 481999.1 1476972H1 260 455 43 481999.1 4211180H1 642 873 43 481999.1 g3665013 371 434 43 481999.1 5153580H1 813 1066 43 481999.1 g2141617 440 513 43 481999.1 1509479H1 819 997 46 338992.1 5510632H1 1 202 46 338992.1 4782751F6 127 187 46 338992.1 4782751H1 127 372 46 338992.1 2987413H1 192 478 46 338992.1 6064208H1 204 465 46 338992.1 g1984325 272 505 46 338992.1 g3239921 294 653 46 338992.1 g2026718 300 591 46 338992.1 g2816869 321 569 46 338992.1 4760384H1 492 580 46 338992.1 4760384F6 492 965 46 338992.1 1305496F6 802 1270 46 338992.1 1305496H1 802 945 46 338992.1 3617505H1 823 1024 46 338992.1 g875546 878 1132 46 338992.1 g669800 877 1199 46 338992.1 g874649 878 1180 46 338992.1 g771213 1011 1062 46 338992.1 3211592H1 1056 1292 46 338992.1 093259H1 1081 1322 46 338992.1 926880H1 1123 1363 46 338992.1 1366443H1 1137 1385 46 338992.1 1366443R6 1137 1466 46 338992.1 4960778H1 1160 1431 46 338992.1 4625867H1 1224 1487 46 338992.1 3383444H1 1259 1504 46 338992.1 5640688H1 1417 1657 46 338992.1 4030718H1 1568 1830 46 338992.1 4030718F6 1568 1945 46 338992.1 2742284H1 1620 1870 51 206603.1 g3278540 1 465 51 206603.1 g4390504 25 492 51 206603.1 g3870096 41 504 51 206603.1 g1109407 277 604 51 206603.1 5631413H1 367 608 51 206603.1 5631413F6 367 812 51 206603.1 1992082H1 531 726 51 206603.1 6092061H1 626 906 52 435694.2 4936540H1 1112 1364 52 435694.2 5021371H1 1139 1417 52 435694.2 3726226H1 1155 1450 52 435694.2 g2015121 1170 1366 52 435694.2 456419H1 1185 1425 52 435694.2 461227R6 1185 1685 52 435694.2 456301H1 1185 1433 52 435694.2 461227H1 1185 1446 52 435694.2 460920H1 1185 1432 52 435694.2 461106H1 1185 1440 52 435694.2 457987H1 1185 1424 52 435694.2 458221H1 1185 1435 52 435694.2 454834R1 1185 1705 52 435694.2 461049H1 1185 1425 52 435694.2 454834H1 1185 1424 52 435694.2 4957324H1 266 486 52 435694.2 3390485H1 267 486 52 435694.2 1437407H1 243 486 52 435694.2 5902323H1 243 486 52 435694.2 3676724H1 271 486 52 435694.2 1437407F6 243 486 52 435694.2 1436837H1 243 480 52 435694.2 5900454H1 243 486 52 435694.2 2706491H1 270 566 52 435694.2 2837043H1 244 486 52 435694.2 3165547H1 246 486 52 435694.2 5903233H1 247 568 52 435694.2 3687630H1 251 565 52 435694.2 4268779H1 252 486 52 435694.2 3460048H1 251 487 52 435694.2 3077826H1 253 501 52 435694.2 4121058H1 271 486 52 435694.2 4900932H1 273 562 52 435694.2 3615215F6 280 731 52 435694.2 832322H1 252 486 52 435694.2 3615215H1 280 588 52 435694.2 2406515H1 254 486 52 435694.2 3141771H1 327 608 52 435694.2 3615215T6 351 720 52 435694.2 g1774842 351 728 52 435694.2 3932194H1 351 486 52 435694.2 4003539H1 351 589 52 435694.2 g587196 351 593 52 435694.2 1285417F6 400 708 52 435694.2 1285417H1 400 637 52 435694.2 2763950H1 502 762 52 435694.2 2415062H1 512 710 52 435694.2 2415070H1 512 702 52 435694.2 3860483H1 617 813 52 435694.2 g1766458 520 850 52 435694.2 g3076400 519 940 52 435694.2 823127H1 556 831 52 435694.2 g3190613 562 745 52 435694.2 2926224H2 688 999 52 435694.2 2708490H1 690 942 52 435694.2 g4311248 702 1175 52 435694.2 g4389608 707 1164 52 435694.2 g3700432 738 1174 52 435694.2 g1773867 738 1172 52 435694.2 1285417T6 758 904 52 435694.2 g4111706 797 1172 52 435694.2 774013H1 825 1036 52 436694.2 1454843H1 899 1163 52 435694.2 1450887F1 899 1172 52 435694.2 3742523H1 896 1163 52 435694.2 1450887H1 899 1152 52 435694.2 3742566H1 899 1163 52 435694.2 1454843T6 913 1128 52 435694.2 4710458H1 961 1249 52 435694.2 4977443H1 1005 1268 52 435694.2 3237593H1 1060 1304 52 435694.2 4705379T6 1071 1144 52 435694.2 4853112H1 1100 1295 52 435694.2 2666646T6 1628 2175 52 435694.2 2959842H1 1635 1861 52 435694.2 2963934T6 1633 2162 52 435694.2 3639070H1 1655 1967 52 435694.2 4322530H1 1660 1782 52 435694.2 5062716H1 1673 1795 52 435694.2 1710033H1 1703 1959 52 435694.2 5021371T1 1715 2162 52 435694.2 3894718H1 1752 1968 52 435694.2 2151922H1 1765 2018 52 435694.2 g1645818 1810 2162 52 435694.2 2323908H1 1816 1878 52 435694.2 g4070415 1817 2162 52 435694.2 g4175351 1821 2162 52 435694.2 g3595864 1824 2162 52 435694.2 g3434496 1843 2162 52 435694.2 g1775010 1845 2162 52 435694.2 g1645819 1872 2162 52 435694.2 g1164565 1885 2262 52 435694.2 4701327H1 1906 2173 52 435694.2 g1766363 1910 2162 52 435694.2 2253564R6 1939 2171 52 435694.2 2253564H1 1939 2195 52 435694.2 4540530H1 1951 2181 52 435694.2 4540144H1 1953 2199 52 435694.2 1833058H1 1959 2171 52 435694.2 g3003709 1979 2171 52 435694.2 g3959558 1980 2162 52 435694.2 g2358889 2057 2171 52 435694.2 g4264824 2059 2162 52 435694.2 474448H1 2096 2171 52 435694.2 4615243H1 1 250 52 435694.2 2533844H1 21 246 52 435694.2 g3154852 56 491 52 435694.2 4270549H1 86 338 52 435694.2 3330903H1 114 331 52 435694.2 4315068H1 219 423 52 435694.2 4315053H1 221 486 52 435694.2 4706408H1 242 486 52 435694.2 1436837F1 243 695 52 435694.2 5900458H1 243 486 52 435694.2 5903501H1 242 486 52 435694.2 5903201H1 243 486 52 435694.2 5426328H1 1199 1361 52 435694.2 g1989927 1223 1525 52 435694.2 g1989319 1223 1632 52 435694.2 g572779 1276 1621 52 435694.2 4611420H1 1351 1610 52 435694.2 4243682H1 1370 1625 52 435694.2 5868132H1 1375 1642 52 435694.2 792533H1 1412 1646 52 435694.2 g1775555 1428 1811 52 435694.2 1469570H1 1472 1684 52 435694.2 1469570F6 1472 1787 52 435694.2 2461531H1 1485 1710 52 435694.2 g2220895 1488 1893 52 435694.2 g1196070 1498 1783 52 435694.2 3561975H1 1527 1843 52 435694.2 1830391H1 1583 1847

[0886]

1 104 1 756 DNA Homo sapiens misc_feature Incyte ID No 061149.1.j 1 gagaaatcca acaagctgct gctagctttg gtgatgctct tcctatttgc cgtgatcgtc 60 ctccaatacg tgtgccccgg cacagaatgc cagcncctcc gcctgcaggc gttcagctcc 120 ccggtgccgg acccgtaccg ctcggaggat gagagctccg ccaggttcgt gccccgctac 180 aatttcaccc gcggcgacct cctgcgcaag gtagacttcg acatcaaggg cgatgacctg 240 atcgtgttcc tgcacatcca gaagaccggg ggcaccactt tcggccgcca cttggtgcgt 300 aacatccagc tggagcagcc gtgcgagtgc cgcgtgggtc agaagaaatg cacttgccac 360 cggccgggta agcgggaaac ctggctcttc tccaggttct ccacgggctg gagctgcggg 420 ttgcacgccg actggaccga gctcaccagc tgtgtgccct ccgtggtgga cggcaagcgc 480 gacgccaggc tgagaccgtc cagcctgcag cagaatcacc tggcgaggag gtgcctgttg 540 aaaaagataa gaagtttcat tcagaaaaga tgaccctgaa gtaaggcaat gagcttccaa 600 aagtcttctc agtgcaatca ccaggcaaat tttataaggc agtcaagaag tttacctaga 660 aataaaaaaa ctcaagagac aataatagtg attaaagtta aatttgatcc cgttcccata 720 taaatcaatt atttatacac ttaacatcat ttgaga 756 2 982 DNA Homo sapiens misc_feature Incyte ID No 404508.3.j 2 gagagaggat gactgcgcga gaagaagcta gcttacgaac acttgaaggc agacgacgtg 60 ccaccttgct tagcgcccgt caaggaatga tgtctgcacg aggagacttc ctaaattatg 120 ctctgtctct aatgcggtct cataatgatg agcattctga tgttcttcca gttttggatg 180 tttgctcatt gaagcatgtg gcatangttt ttcaagcact tatatactgg attaaggcaa 240 tgaatcagca gacaacattg gatacacctc aactagaacg caaaaggacg cgagaactct 300 tggaactggg tattgataat gaagattcag aacatgaaaa tgatgatgac accaatcaaa 360 gttagtgcac agaaaatctg ctaatctact tcaagaaatg gctgcctcag tagttcccct 420 tcaagctttt taacttcatt attttctgtc tgggtgggaa tttctctttt cttctctatg 480 tctcatttct tacattttct gtccattttt gcttacacat tcttgcgtta tacatttcac 540 aactaaggat gtattaaaga aatgttataa actttccaac aatatttttt cttctatctt 600 ttcttgtatt tgtcttagta ttatgtttac ctttactctt aatatactct tattacattt 660 aataaaatct tagcaaaacc gttgttaata ttgatgcaaa atagatttaa tcaagaaaat 720 gagaattacc agttacagct cccaaatatc agaacgctag caattaatac aatgaaaaga 780 gaaaatatcc caactccaga cttttctcca aaagttttaa tatcacactt tggggtctag 840 tggagtttat ttgtgggttg cagttatttc aaatgggact aaataatgca ttctccagtt 900 tcttattatc aactagtact tttattcagc ctatggaaag acagttggcc taattgctgt 960 tttgagaacc cagccatagc tc 982 3 1039 DNA Homo sapiens misc_feature Incyte ID No 441227.2.j 3 gcggcgccgg ggattgggag ggcttcttgc aggctgctgg gctggggcta agggctgctc 60 agtttccttc agcggggcac tgggaagcgc catggcactg cagggcatct cggtcatgga 120 gctgtccggc ctggccccgg gcccgttctg tgctatggtc ctggctgact tcggggcgcg 180 tgtggtacgc gtggaccggc ccggctcccg ctacgacgtg agccgcttgg gaccggggca 240 agcgctcgct agtgctggac ctgaagcagc cgcggggagc cgccgtgctg cggcgtctgt 300 gcaagcggtc ggatgtgctg ctggagccct tccgccgcgg tgtcatggag aaactccagc 360 tgggcccaga gattctgcag cgggaaaatc caaggcttat ttatgccagg ctgagtggat 420 ttggccagtc aggaagcttc tgccggttag ctggccacga tatcaactat ttggctttgt 480 caggtgttct ctcaaaaatt ggcagaagtg gtgagaatcc gtatgccccg ctgaatctcc 540 tggctgactt tgctggtggt ggccttatgt gtgcactggg cattataatg gctctttttg 600 accgcacacg cactgacaag ggtcaggtca ttgatgcaaa tatggtggaa ggaacagcat 660 atttaagttc ttttctgtgg aaaactcaga aatcgagtct gtgggaagca cctcgaggac 720 agaacatgtt ggatggtgga gcacctttct atacgactta caggacagca gatggggaat 780 tcatggctgt tggagcaata gaaccccagt tctacgagct gctgatcaaa ggacttggac 840 taaagtctga tgaacttccc aatcagatga gcatggatga ttggccagaa atgaagaaga 900 agtttgcaga tgtatttgca aagaagacga aggcagagtg gtgtcaaatc tttgacggca 960 cagatgcctg tgtgactccg gttctgactt ttgaggaggt tgttcatcat gatcacaaca 1020 aggaacgggg ctcgtttat 1039 4 1673 DNA Homo sapiens misc_feature Incyte ID No 277927.2 4 ggcagttgta aagtcgctgg ccagctagtg gagtggagac tgcagaggga gataaagaga 60 gagggcaaag aggcagcaag agatttgtcc tggggatcca gaaacccatg ataccctact 120 gaacaccgaa tcccctggaa gcccacagag acagagacag caagagaagc agagataaat 180 acactcacgc caggagctcg ctcgctctct ctctctctct ctcactcctc cctccctctc 240 tctctgcctg tcctagtcct ctagtcctca aattcccagt cccctgcacc ccttcctggg 300 acactatgtt gttctccgcc ctcctgctgg aggtgatttg gatcctggct gcagatgggg 360 gtcaacactg gacgtatgaa ggcccacatg gtcaggacca ttggccagcc tcttaccctg 420 agtgtggaaa caatgcccag tcgcccatcg atattcagac agacagtgtg acatttgacc 480 ctgatttgcc tgctctgcag ccccacggat atgaccagcc tggcaccgag cctttggacc 540 tgcacaacaa tggccacaca gtgcaactct ctctgccctc taccctgtat ctgggtggac 600 ttccccgaaa atatgtagct gcccagctcc acctgcactg gggtcagaaa ggatccccat 660 gtgggtcaga acaccagatc aacagtgaag ccacatttgc agagctccac attgtacatt 720 atgactctga ttcctatgac agcttgagtg aggcttgctg agaggcctca gggcctggct 780 gtcctgggca tcctaattga ggtgggtgag actaagaata tagcttatga acacattctg 840 agtcacttgc atgaagtcag gcataaagat cagaagacct cagtgcctcc cttcaaccta 900 agagagctgc tccccaaaca gctggggcag tacttccgct acaatggctc gctcacaact 960 cccccttgct accagagtgt gctctggaca gttttttata gaaggtccca gatttcaatg 1020 gaacagctgg aaaagcttca ggggacattg ttctccacag aagaggagcc ctctaagctt 1080 ctggtacaga actaccgagc ccttcagcct ctcaatcagc gcatggtctt tgcttctttc 1140 atccaaggat cctcgtatac cacaggaaga agaggctgga aaaccgaaag agtgtggtct 1200 tcacctcagc acaagccacg actgaggcat aaattccttc tcagatacca tggatgtgga 1260 tgacttccct tcatgcctat caggaagcct ctaaaatggg gtgtaggatc tggccagaaa 1320 cactgtagga gtagtaagca gatgtcctcc ttcccctgga catctcctag agaggaatgg 1380 acccaggctg tcattccagg aagaactgca gagccttcag cctctccaaa catgtaggag 1440 gaaatgagga aatcgctgtg ttgttaatgc agagaacaaa ctctgtttag ttgcagggga 1500 agtttgggat ataccccaaa gtcctctacc ccctcacttt tatggccctt tccctagata 1560 tactgcggga tctctcctta ggataaagag ttgctgttga agttgtatat ttttgatcaa 1620 tatatttgga aattaaagtt tctgacttta aaaaaaaaaa aaaaaaaaaa aaa 1673 5 968 DNA Homo sapiens misc_feature Incyte ID No 475311.1 5 ccgcgtcgat cctgggatgg aggaggtggc ggccgctgag gctcggcgtg aagacggcgg 60 gcatggtggg gcgggagaaa gagctctcta tacactttgt tcccgggagc tgtcggctgg 120 tggaggagga agttaacatc cctaatagga gggttctggt tactggtgcc actgggcttc 180 ttggcagagc tgtacacaaa gaatttcagc agaataattg gcatgcagtt ggctgtggtt 240 tcagaagagc aagaccaaaa tttgaacagg ttaatctgtt ggattctaat gcagttcatc 300 acatcattca tgattttcag ccccatgtta tagtacattg tgcagcagag agaagaccag 360 atgttgtaga aaatcagcca gatgctgcct ctcaacttaa tgtggatgct tctgggaatt 420 tagcaaagga agcagctgct gttggagcat ttcctcatct acattagctc agattatgta 480 tttgatggaa caaatccacc ttacagagag gaagacatac cagctcccct aaatttgtat 540 ggcaaaacaa aattagatgg agaaaaggct gtcctggaga acaatctagg agctgctgtt 600 ttgaggattc ctattctgta tggggaagtt gaaaagctcg aagaaagtgc tgtgactgtt 660 atgtttgata aagtgcagtt cagcaacaag tcagcaaaca tggatcactg gcagcagagg 720 ttccccacac atgtcaaaga tgtggccact gtgtgccggc agctagcaga gaagagaatg 780 ctggtaagaa ggattcctga gtcctgtctt agcgaaggtc cgctttgtct tttccatgct 840 tgaactttca cagctgtact tggagtgtta ctgagtgaaa gccaaaagtg cttttttaaa 900 actaggagac caaacaaaag tagtttacat atacactgta ttcatgaaga ataaaaatat 960 tatgctct 968 6 3968 DNA Homo sapiens misc_feature Incyte ID No 013039.2 6 cccaaagcaa aagaaataca gttacgatgg ggaccccctc tggttgatgg tggatcaccc 60 atttcctgtt acagtgtgga aatgtctcct atagaaaaag atgaacctag agaagtttac 120 caaggttctg aagtagaatg tacagtgagc agccttcttc ctggaaagac atacagcttc 180 agactacgtg cagctaacaa aatggggttt ggaccatttt cagaaaaatg tgatattact 240 acagcccctg ggccaccaga tcagtgcaag ccccctcaag tgacatgtag atctgcaact 300 tgtgcacaag tgaattggga ggttcctttg agtaatggaa cagatgtcac tgaatatcga 360 ctggagtggg gaggagttga aggaagtatg cagatatgtt actgtgggcc tggtctcagt 420 tatgaaataa aaggactttc accagcaact acctattatt gcagggtcca ggctctgagt 480 gttgtgggtg caggcccttt cagtgaagta gtagcctgtg tgactccacc atcagttcct 540 ggcattgtga cctgtcttca agaaataagc gatgatgaga tagaaaatcc ccattattca 600 ccttctacat gccttgcaat aagctgggaa aagccttgtg atcatggttc ggaaatcctt 660 gcctacagca tagactttgg agataaacaa tccctaacag tgggaaaggt tacaagctat 720 attatcaaca atttgcaacc agatacaaca tacagaatac gaattcaagc cttgaatagc 780 cttggagctg gtcctttcag ccatatgata aaattaaaaa ctaagcctct ccctcctgat 840 ccacctcgtc tggaatgtgt tgcctttagc caccagaacc ttaagctgaa atggggagaa 900 ggaactccaa agacattgtc aaccgattct attcagtacc accttcagat ggaggataag 960 aatggacggt ttgtatccct atacagagga ccatgtcata catacaaagt acaaagactt 1020 aatgagtcaa catcctataa attctgtatt caagcttgta atgaagctgg ggaaggtccc 1080 ctctcccaag aatatatttt cactactcca aaatctgtcc cagctgcctt gaaagccccc 1140 aaaatagaga aagtaaatga tcacatttgt gaaattacat gggagtgttt acagccaatg 1200 aaaggtgatc cagttattta cagtcttcaa gttatgttgg gaaaagattc agaattcaaa 1260 cagatttaca agggtcccga ctcttccttc cggtattcca gccttcagct gaactgtgaa 1320 tatcgcttcc gtgtatgtgc cattcgccag tgccaagact ctctgggaca ccaggacctc 1380 gtaggtccct acagcaccac agtgctcttc atctctcaga ggactgaacc accagccagc 1440 accaacagag acactgtgga aagcacaagg acccgacggg cactgagtga cgagcagtgt 1500 gctgccgtca tccttgtgct gtttgctttc ttttccattt tgattgcctt tatcattcag 1560 tactttgtaa tcaagtgaaa atataacttt attttttaac tctattacat tttattttgt 1620 catgtactaa aattatttct gtattgcttt tataaaaaac agtggcattt agcactggca 1680 ttgagactat agcacatcat ttttgccatt ttcagtgctt atattgttag gtagaggctg 1740 gcactttatt agaatgcaag ccacaaaaat atcaattttg ttttttttgt tagggtgggt 1800 cttctttttt tctttccctc tctctttttt taacaaatgc cttcttatag aaaaactttc 1860 taagaggcaa caatttagaa tggatatttt gacgaatcgg catgagtgta acagtgataa 1920 cctgatgctg tttgttttaa agattattac caagtgaaaa attcagaatg aatagaattt 1980 acactaacat gctatataaa atgttaaagt ctgatgctgt gaaagcaatc tagtgctata 2040 tttctacctc ctcatttgtc ttaattattt ggtaagtggg attatgatga gtaactggag 2100 gggcttagaa acaaaaactg gatgaaagag tatgcatgaa gaaaagcttc tttgataaat 2160 gtggagttct tcattataaa tatatattca tgaattcaca gataagtact taaagaacag 2220 acagtttact tggcctaaaa atattttgat gtttactcaa aaagtacctc ttcaggtctt 2280 gagaacatgg aaaagaattg agtgctttta aatacttttt agaaagtaat ccataaaagt 2340 aaattgaatt tcaaacctat ttggcttctg ttttgtgaac ctttgaacta tatgtatgtg 2400 tataagggta tacacatacc atatatggca tataacaagt gtacacatat acacataaca 2460 agtgtagaag tatatattac ataacataca ctcactctgt ctggtatagg ctaattttga 2520 agaactccca taagtttctg ctgcttctcc cattaactgc ttgccaccac catcagaatt 2580 cataatcaaa cctaaccttt ttgtttgggg caccaaatct gaagacaaaa ttaatttgca 2640 ccagtaaact tcaagctgct ttctttcttg aaaactaaac gtttaacgta taatgtctgt 2700 ttggatactg ttccaaattg ttgattgcat gtggttaatg ttgcattaga gcactttgca 2760 attgcataat tcattaatgt tttgtgagct tgcatttgtg agttattgga tgatcagact 2820 gaattttgtc aagtatcaca ttgtacatct tgcctagatg tcgatgactg caagtaataa 2880 tacagtttat aatgaaacta tctacaattc ttgttttagc acatctgtta tccgtaaaac 2940 acctgtaact agctttttta atttattatt tgaattttag gatagcgaat cactaatttt 3000 tagttgctga ggttggcatt ttagtgatta ttaagcactt ctgtcagtct ttgaaaaaag 3060 aacgtatttt ttgtggcttt gaagatctct gaagaatttc ttttataata gaatgggcat 3120 gtattgtaac agttttatgt caaatgatct gtgctgtaga aaaacattaa cccttgttca 3180 aaaaagaaat ggataaactt ggcctttcta agtggtaaga atgacctgtc actataatat 3240 actgtatgtt tacattttat ttaaatttaa tctcttatgt atagggtgat aaccttcccc 3300 agaaacaaca gtgattgcga ttgttttcta gaaacttctt taaagtgcca catttggcag 3360 tacaaatgag tctgagtgta atagcccaga gatttatata tagttgaatg tctaaaatgg 3420 taaaatgtgc cactgtgtca agttacagtg gcttatgttt ttcatagtaa ttcaaatgaa 3480 cttcctattt ttgatagtaa atgtcattta atagtatact tgccatttga gcctcactgc 3540 aaaattagtg cagaggagaa aacaattttt aatgtaatct tgattttacc tcatatactg 3600 tacattccaa aaactctaaa ctttttaaag attatagata cactaccaaa catatcacct 3660 taaaattgta taaggctgaa tgaacttcat acaaatgaaa aaaatctcat aaaaatacat 3720 aaactatgta gcaaaagtat ctgtaaaatc catggaaaat aaaagttgta tcattctttt 3780 tgagatacgt ttattgtatt catatatatt cattatttgc tacctgttta agaaagtgaa 3840 atgttatggt ctcccctctt ccaatgagct taaaacattt ttcccaacag tatataaatc 3900 ttcaacatga gaggatgtat atttattata taaagcccag taaagaataa aattagaagt 3960 tttatcct 3968 7 1937 DNA Homo sapiens misc_feature Incyte ID No 238005.4 7 ccgttttcnc aatttgggct ggacgaaaaa nacggtcttg ctttcccggt cgccgctgtc 60 gggaagggct gcagggtgtc cgcgagaccc gcggcccggc gagctgaccc cgcctcgcct 120 ttcctgccta gccctcattc cacggagccg gtcgcgcccg gtccttgcgc gacgcttccc 180 ggcccaggcc gcctggtctg gcgctggagg ccggagtccc gcggcctgtg ctggatccgc 240 gcacacccag tggcggcgga tgggcggccg gggcggccgg ggcggccggt cctgagcgcg 300 gcccgggctg tcagggctgg ctgctggcgg gatggacacc ctggaggagg tgacttgggc 360 caatgggagc acagcgctac ccccacccct ggcaccaaac atcagtgtgc ctcatcgctg 420 cctgctgctg ctctacgaag acattggcac ctccagggtc cggtactggg acctcttgct 480 gctcatcccc aatgtgctct tcctcatctt cctgctctgg aagcttccat ctgctcgggc 540 gaagatccgc atcacctcca gccccatttt tatcaccttc tacatcctgg tgtttgtggt 600 ggcgctggtg ggcattgccc gggccgtggt atccatgacg gtgagcacct cgaacgctgc 660 aactgttgct gataagatcc tgtgggagat cacccgcttc ttcctgctgg ccatcgagct 720 gagtgtgatc atcctggggc ctggcctttg gccacctgga gagtaagtcc agcatcaagc 780 gggtgctggc catcaccaca gtgctgtccc tggcctactc tgtcacccag gggaccctgg 840 agatcctgta ccctgatgcc catctctcag ctgaggactt taatatctat ggccatgggg 900 gccgccagtt ctggctggtc agctcctgct tcttcttcct ggtctactct ctggtggtca 960 tccttcccaa gaccccgctg aaggagcgca tctccctgcc ttctcggagg agcttctacg 1020 tgtatgcggg catcctggca ctgctcaacc tactgcaggg gctggggagt gtgctgctgt 1080 gcttcgacat catcgagggg ctctgctgtg tagatgccac aaccttcctg tacttcagct 1140 tcttcgctcc gctcatctac gtggctttcc tccggggctt cttcggctcg gagcccaaga 1200 tcctcttctc ctacaaatgc caagtggacg agacagagga gccagatgta cacctacccc 1260 agccctacgc tgtggcccgg cgggagggcc tggaggctgc aggggctgct ggggcctcag 1320 ctgccagcta ctcgagcacg cagttcgact ctgccggcgg ggtggcctac ctggatgaca 1380 tcgcttccat gccctgccac actggcagca tcaacagcac agacagcgag cgctggaagg 1440 ccatcaatgc ctgagggcag ctgccagggc ctgtggagga caggccagag aggaggccag 1500 caggccccag agtccccagg ggaggaggac caggtcaagg gacgttctgt gggcagtagc 1560 cctgtgtggc cctgttccca ccatgagtct ggaggcccca cctccctggg gctcccaatc 1620 ccctttgcca tctctgctct cactggggac cctcctcccc ttcccacctg ctctcatact 1680 gctcagtgac atggcccagg ctttccttcc agggccatgc ttggcaaggt tggctgaggg 1740 caccctcctt ctctgcaccc ttggcacgag ggcagggctg gctctcccaa tgcctccatc 1800 ccatccccat ggtgctttgg cctcctcaaa gcatccacca tggtggatgg actgaagtgt 1860 gtatattttc ttgatctatt ttttaataaa aaggaaaagg agcagaaaaa aanaaaaann 1920 aaanaanngg aaaaaaa 1937 8 794 DNA Homo sapiens misc_feature Incyte ID No 345322.1.j 8 attagcgtat tgttcctttc tgtattgtgc tgagaggatc caagggattn gtgggggaac 60 aggcaagcca ggcatcaccg tggatgttga agaagggggt tactcaaacc tcggcatctt 120 cacttgctcg atctggaatt acagctattt attacgaagc actctgtgtg gcttagtgga 180 gtgtgtctga ggaaacacat cccggacacc acttagggtt agtctttctg agctcttcac 240 atctctgact aattatcatc attaccatgg agcccaacag tcccaaaaag atacagtttg 300 ccgtgcctgt attccagagt cagattgcac ctgaagcagc agagcagatc aggaaaagaa 360 gacctacacc agcatcactt gtgattctca atgagcataa ccccccagaa atagatgaca 420 agagggggcc caacacacaa ggggaattac agaatgcatc ccctaagcaa aggaagcaga 480 gtgtgtacac accacccacc ataaaagggg ttaagcatct gaaaggccag aatgaatcag 540 cattccctga agaagaagaa ggcaccaatg aaagagagga gcagcgggac cattaattac 600 tggtctgcag caagaaggct tcttggaaat aactgaacta ttaacttttc tgagtatacc 660 atggaattcc actgcttgac ttccagaagc atcctccatc tctgcacccc acactcatac 720 agtagctatg cacatcctgg aagtctcctt gactgaactt tagaactaag tacacattnt 780 ccacancact tata 794 9 3991 DNA Homo sapiens misc_feature Incyte ID No 348094.6.j 9 tttgtagaga ccgtgtctcc ctatgtcgcc caggaaaagg aaactattaa taagcttgga 60 cgaatatgct tcaactctag aattctgaaa aaaatcagaa aactaaaaac ttctgaagct 120 ctatttgaaa tctctcttca aattgagttc taaagttcct gttgcttcag acaatggatg 180 agcaatcaca aggaatgcaa gggccacctg ttcctcagtt ccaaccacag aaggccttac 240 gaccggatat gggctataat acattagcca actttcgaat agaaaagaaa attggtcgcg 300 gacaatttag tgaagtttat agagcagcct gtctcttgga tggagtacca gtagctttaa 360 aaaaagtgca gatatttgat ttaatggatg ccaaagcacg tgctgattgc atcaaagaaa 420 tagatcttct taagcaactc aaccatccaa atgtaataaa atattatgca tcattcattg 480 aagataatga actaaacata gttttggaac tagcagatgc tggcgaccta tccagaatga 540 tcaagcattt taagaagcaa aagaggctaa ttcctgaaag aactgtttgg aagtattttg 600 ttcagctttg cagtgcattg gaacacatgc attctcgaag antcatgcat agagatataa 660 aaccagctaa tgtgttcatt acagccactg gggtggtaaa acttggagat cttgggcttg 720 gccggttttt cagctcaaaa accacagctg cacattcttt agttggtacg ccttattaca 780 tgtctccaga gagaatacat gaaaatggga tacaacttca aatctgacat ctggtctctt 840 gggctgtcta ctatatgaga tggctgcatt acaaagtcct ttctatggtg acaaaatgaa 900 tttatactca ctgtgtaaga agatagaaca gtgtgactac ccacctcttc cttcagatca 960 ctattcagaa gaactccgac agttagttaa tatgtgcatc aacccagatc cagagaagcg 1020 accagacgtc acctatgttt atgacgtagg caaagaggat gcatgcatgc actggcaagc 1080 agctaaaaca ttgcaagatc atgaagagtg taaccaaagt aattgaaagt attttgtgca 1140 agtcgtacct ccccatttat gtctggtgtt aagattaata tttcagagct agtgtgcttt 1200 gaatccttaa ccagttttca tataagcttc attttgtacc agtcacctaa atcacctcct 1260 tgcaaccccc aaatgacttt ggaataactg aattgcatgt taggagagaa aatgaaacat 1320 gatggttttg aatggctaaa ggtttataga atttcttaca gttttctgct gataaattgt 1380 gtttagatag actgtcagtg ccaaatattg aaggtgcagc ttggcacaca tcagaataga 1440 ctcatacctg agaaaaagta tctgaacatg tgacttgttt cttttttagt aatttatgga 1500 cattgagatg aacacaattg tgaacttttg tgaagatttt atttttaaac gtttgaagta 1560 ctagttttag ttcttagcag agtagttttc aaatatgatt cttatgataa atgtagacac 1620 aaactatttg agaaacattt agaactctta gcttatacat tcaaaatgta actattaaat 1680 gtgaagattt ggggacaaaa tgtgagtcag acactgaaga gttttttgtt ttgttttaat 1740 atttttgata ttctctttgc attgaaatgg tataaatgaa tccatttaaa aagtggttaa 1800 ggatttgttt agctggtgtg ataataattt ttaaagttgc acattgccca aggctttttt 1860 tgtgtgtttt tattgttgtt tgtacatttg aaaaatattc tttgaataac cttgcagtac 1920 tatatttcaa tttctttata aatttaagtg cattttaact cataattgta cactataata 1980 taagcctaag tttttattca taagttttat tgaagttctg atcggtcccc ttcagaaatt 2040 tttttatatt attcttcaag ttactttctt atttatattg tatgtgcatt ttatccatta 2100 atgtttcata ctttctgaga gtataatacc cttttaaaag atatttggta taccaatact 2160 tttcctggat tgaaaacttt ttttaaactt tttaaaattt gggccactct gtatgcatat 2220 gtttggtctt gttaaagagg aagaaaggat gtgtgttata ctgtacctgt gaatgttgat 2280 acagttacaa tttatttgac aaggttgtaa ttctagaata tgcttaataa aatgaaaact 2340 ggccatgact acagccagaa ctgttatgag attaacattt ctattgagaa gcttttgagt 2400 aaagtactgt atttgttcat gaagatgact gagatggtaa cacttcgtgt agcttaagga 2460 aatgggcaga atttcgtaaa tgctgttgtg cagatgtgtt ttccctgaat gctttcgtat 2520 tagtggcgac cagtttctca cagaattgtg aagcctgaag gccaagagga agtcactgtt 2580 aaaggactct gtgccatctt acaaccttgg atgaattatc ctgccaacgt gaaaacctca 2640 tgttcaaaga acacttccct ttagccgatg taactgctgg ttttgttttt catatgtgtt 2700 tttcttacac tcatttgaat gctttcaagc atttgtaaac ttaaaaaatg tataaagggc 2760 aaaaagtctg aacccttgtt ttctgaaatc taatcagtta tgtatggttt ctgaagggta 2820 attttatttt ggaataggta aaggaaacct gttttgtttg tttttcctga gggctagatg 2880 catttttttt ctcacactct taatgacttt taacatttat actgagcatc catagatata 2940 ttcctagaag tatgagaaga attattctta ttgaccatta atgtcatgtt cattttaatg 3000 taatataatt gagatgaaat gttctctggt tggaacagat actctctttt tttttcttgc 3060 aatctttaag aatacataga tctaaaattc attagcttga cccctcaaag taacttttaa 3120 gtaaagatta aagcttttct tctcagtgaa tatatctgct agaaggaaat agctgggaag 3180 aatttaatga tcagggaaat tcattatttc tatatgtgga aactttttgc ttcgaatatt 3240 gtatcttttt aaatctaaat gttcatattt ttcctgaaga aaccactgtg taaaaatcaa 3300 attttaattt tgaatggaat aatttcaaag aactatgaag atgatttgaa gctctaattt 3360 atatagtcac ctataaaatg ttctttatat gtgttcataa gtaaatttta tattgattaa 3420 gttaaacttt tgaattgatt tgaggagcag taaaatgaaa gctatatcta ttctaaacct 3480 tatttagaca ttggtaccag ttacccaggt gaaaatatgg agtaactttg ttttgtatgg 3540 taaggtttag gaatggtgga tgaagggtat ctctatataa ataaagtgct caacaatgtg 3600 caatgattgt aaatttagta agatattaca gccatttcat gaatgcttta ccattcaaca 3660 tagtatctat tacaaaacac ctttcttgta tccatatact tcaggtgttg ctgttaacat 3720 ttactatgat atttatttta accaaaatgt tactcacatt aaatgtttat tctttaaaat 3780 gaatgtatta tgtttttaac ccacaaatgc atacttaccc tgtgcctcat atttcaatag 3840 tactgtaata tggacatctt ttgtgaaata cttttatttt gttatgcttt aaatatacat 3900 acaaaaagat ttctgttatt agctttgaaa attgtataat atcctaatat aaacaaaaat 3960 ataaaaataa aaatgaatac agtaaaatgt c 3991 10 2885 DNA Homo sapiens misc_feature Incyte ID No 233678.1 10 aaatagtaag aaaataatgt acagttggta ctcagatgtg gggcctaagc tatgaatggg 60 actagagcat tgctacaggt tgggcattgc tgggcactgt atgtaggtcg cctgacccta 120 tctcccatgg gagtgatgac cagtcccaga ggcctgtgtg actctgaatc ttccaacctc 180 acaggccatt ccctcccttc tgaaagccca cccatgggct tctggcccct gtccaaggcg 240 tgggagggag gccacggcct ctgatgcacc tgggcgtccc ctcccatccc ccctccctgc 300 acaggtgctg gaaacatgca tgaagagctg cggcaagcgg ttccacgacg aagtgggcaa 360 gttccgcttt ctcaacgagc tcatcaaggt cgtgtctccc aagtatctgg gctctcggac 420 atcggagaag gtgaagaaca agatcttgga gctcctctac agctggacag tgggcctgcc 480 cgaggaggtg aaaatcgcag aggcctacca gatgctaaag aagcagggga ttgtaaagtc 540 cgaccccaag cttccagatg acactacctt tccccttcct cctccacggc cgaagaatgt 600 gatctttgaa gatgaggaga aatccaagat gctggcccgc ctgctgaaga gctcccatcc 660 cgaagacctc cgcgcaccaa taagctcatc aaagagatgg tgcaggagga ccagaagcgg 720 atggagaaga tctcgaagag gggtgaatgc catcgaggag gtgaacaaca atgtgaaact 780 ggctcacgga gatggtgatg agccacagcc agggcggcgc acagctggca gcagcgagga 840 cctcatgaag gaactgtacc agcgctgtga gcggatgcgg cccacgctct tccgactggc 900 gagtgacaca gaggacaatg atgaggcctt agcggagatc ctgcaggcca atgacaacct 960 cacccaggtg atcaacctgt ataagcagct ggtgcggggt gaggaggtca acggtgatgc 1020 cacagccggc tccatccctg gggagcacct cggccctgct ggatctctca ggcctggatc 1080 tcccgcctgc gggcaccacc tacccagcta tgcccacccg ccctggcgag caggccagcc 1140 ctgagcagcc cagtgcctca gtttccctgc ttgacgacga gctcatgtct ctgggcctca 1200 gtgaccccac acccccttca ggcccaagcc tggatggtac cggatggaac agcttccagt 1260 cgtcggatgc cactgagccc ccagcccctg ctctgggccc aggcccccag tatggaaagc 1320 cgacccccag cgcagacatc cctgccagca agcagcggtc tggacgacct agacctcctg 1380 gggaagaccc tcctgcagca gtcgctgccc ccggaatccc agcaagtgcg gtgggagaag 1440 cagcagccaa ccccccggct cacactccgg gacctgcaga ataagagcag cagctgcagc 1500 tcccccagct ccagcgccac cagccttctc cacaccgtgt ccccagagcc ccccaggcct 1560 ccgcagcagc ccgtaccaac cgagctctca ctggccagca tcactgtgcc cctggagtcc 1620 atcaaaccca gcaacatcct gcccgtgact gtgtatgacc agcacggctt ccgcatcctc 1680 ttccattttg cccgggaccc actgccaggg cgctccgacg tgctggtggt ggtggtttcc 1740 atgctgagca ccgcccccca gcccatccgc aacatcgtgt tccagtcagc tgtccccaag 1800 gttatgaagg tgaagctgca gccaccctcg ggcacggagc tgccagcttt taaaccccat 1860 cgtccacccc tcagcaatca cccaggtcct gctgcttgcc aacccccaga aggagaaggt 1920 tcgcctccgc tacaagctca ccttcaccat gggtgaccag acctacaacg agatggggga 1980 tgtggaccag ttccccccac ctgaaacctg gggtagcctc tagaacagag gggctgggga 2040 gaggaagggg cagagggacc ggtcactgtc cagcctggag ggaggcattg gtggccaagg 2100 acaccctttg ttgcccatgg ccattcaccc ccaggcctgg tgcttctccc cacacccctg 2160 taggcctcaa gtgactcttc cccctcctgc tccggccccg cccctgctga gccaaaccca 2220 gtaggaggct ggggcctggg tttgtgccgc tggggtctcc atcaccggga cctggagagg 2280 gaggggctgt gtagccttgg aagaacttgg gtcatgggga ggaagcacag ctgttgggga 2340 agggccagga cctcaggccc agccccaacc ccagctgggg tggggtcttc cccacctgtc 2400 tcttatgcct tatgggaagg cccagccata actcgggggc catgctggag ctggggacca 2460 gcttaggcct cctccatagg aacccagtga ctggggggtg acgcctacac ccccagctat 2520 ttgcactctg gtgtgtggtt tgactctgct tttcttccgg attggccctg tggtcacagc 2580 ctcagggggc cagggctggg ggaacctcac ctggcccgta ctcctggggg tttccctttg 2640 ccattgggcc ccctgaggga ctgtgggggc tcaagggtaa tgccagaggc ccatggcccc 2700 agcgaggggc tgtggggcac ctagagttct cggtgtgtct ccttcattca ttggcctctg 2760 ctggggcctc ctatgggtgt cttacgtctg tccatccatc tgtccgtggt cagaagtggg 2820 gtcagtgtgt gagtgagagc aggagtattt atgaaaataa aacgtcgttt ttcctggaaa 2880 aaaaa 2885 11 2458 DNA Homo sapiens misc_feature Incyte ID No 312243.1 11 ggggcctcac aggccacgtg agcttctgag agctctgagc atgaggtcac gggctcccag 60 aggcagtgat gtggcagcgc ctgtctcccg ccccccgtcc agctccgacg ccggcctgcg 120 gttcccggac agcaacggcc tcctgcagac cccacgctgg gacgagccgc agcgggtgtg 180 cgccctggag cagatttgcg gcgtgttccg cgtggatctg ggccacatgc gctccctccg 240 ccttttcttc agcgacgagg cctgcaccag cggccagctg gtcgttgcca gccgagagag 300 ccagtacaag gttttccact tccaccacgg cggcctggac aagctgtctg acgtgttcca 360 gcagtggaaa tactgcaccg agatgcagct caaagaccag caggtcgccc ccgataagac 420 atgcatgcag ttctccatcc gccgccccaa gctgccgtcc tccgagacgc accccgagga 480 gagcatgtac aagaggctcg gcgtctccgc ctggctcaac cacctgaatg agctgggcca 540 ggtggaggag gagtacaagc tgcggaaggc cattttcttt ggcggtattg atgtgtcaat 600 ccgcggggag gtctggccct tcctgctgcg ctattacagc cacgagtcca cgtcggagga 660 gcgggaggcg ctgcggctgc agaagcgaaa ggagtactct gagatccagc agaaaaggct 720 ctccatgact cccgaggagc acagagcgtt ctggcgtaat gtgcagttca ctgtggacaa 780 agacgtggtc cggacagatc ggaacaacca gttcttccgg ggggaagaca atcccaatgt 840 ggagagcatg aggaggatcc tgctgaacta cgccgtgtac aaccctgccg tcggtattcc 900 caagggatgt cggacctggt ggcgcccatc ttggccgagg tcctggatga gtcagacacc 960 ttctggtgct ttgtgggttt gatgcagaac acgatcttcg tcagctcacc ccgggacgag 1020 gacatggaga aacaactgct gtacctgcgc gagctgctgc ggctgacgca cgtgcgcttc 1080 taccagcacc tggtctcgct gggcgaggac ggcctgcaga tgctcttctg ccaccgctgg 1140 ctccttctgt gcttcaagcg ggagttcccc gaggccgaag cgctgcggat ctgggaggcc 1200 tgctgggccc actaccagac ggactacttc caccttttca tctgcgtggc catcgtggcc 1260 atctacgggg atgacgtcat cgagcagcag ctggccacgg accagatgct cctgcacttc 1320 ggaaacctgg ccatgcacat gaacggggag ctcgttctcc ggaaggcgag gagtttgctg 1380 taccagttcc gcctcctgcc ccggatcccc tgcagcctgc acgatctgtg taagctgtgc 1440 gggtcaggca tgtgggacag cggctccatg cccgcggtgg agtgcaccgg ccaccatccc 1500 ggctcggaga gctgtcccta cgggggcacg gtggagatgc cttcccccaa gtccctgagg 1560 gaaggcaaga agggcccaaa gacgccgcag gacggcttcg gcttccgcag ataggtcggg 1620 cccccgacac cggacagggg ttgaggggac ctcctcagag gccctgggca cgggaggggg 1680 tggggctggg cgtgaagggg acaggggacg atagaaacct aaggaaaatg cttttgggca 1740 acatgagagg aaccttttca tattaatgac aaaattagag tctggaagtg acagaagtca 1800 gatctacagc cacccagagg aaagtcagct cctgaaacgc tgcagtggaa cgcgcagcca 1860 ccgcacctga gacgcaggct ggctgggctc tcctgctggc tgccctggag gatttcaaca 1920 tgtcccagga tttgctccac cctcgagggc agccagacag cgtcgccagg caatgaggaa 1980 agcagagaca ggagaggaag gcctcactca cccactgcgt cgagggctgc agaacacagc 2040 ggggtcctgt ccaggcccag ggacatcttt gcaagccaga cacacttcct cttgagacct 2100 cgttctctcg gagtgagcca aacacacttc ccaaaacgtc cccagccaca gctgggatgc 2160 cgatggaaag gcatctgcca taaaagaaaa gcaaaagata aaaagcccaa ccgatgtggg 2220 gatagagagg cggaagagca gtcaggcttg aggagctggc gcttgtaatg tttatccgtt 2280 taaacatttc gtcctcctgg tacacgaagg gaactgtctg cccaggagcc tgagcctcag 2340 gctgttggag aagcatctga tgcctttttc tttgctgggg gtcttctacg tgaggttcct 2400 tggcgttgtt taaggtcaac tccaccaaat acagcaccca gctggggctt gaatggga 2458 12 748 DNA Homo sapiens misc_feature Incyte ID No 425487.3 12 gcggccgcag cgtcggggct ggagcgatgg cggcgaccgc ggtggcggcg gctgtggcgg 60 gaaccgagtc ggcccagggt cccccgggcc cggcagcgtc gctggagctg tggctgaaca 120 aagccacaga cccaagcatg tcggaacagg attggtcagc tatccagaat ttctgtgagc 180 aggtgaacac tgaccccaat ggccccacac atgcgccctg gctactggcc cacaagatcc 240 agtctccgca agagaaggaa gctctttatg ccttaacggt gagtttggct tgccttgtag 300 cctaaccttt cctgtccttg tgctatagag agccgagagg cgctttgctt ccacacagat 360 ccttttcact ggagaaggga ggtcccctga gaggtttacc ttcacagcag gttggaggag 420 ggagatctgg gccagggtcc ccacccttct tcctcctgtt tctcgtctgt ttcttcaggg 480 cagcattgag tctactgtgg gagaaggaaa ggaaggtttt atttcatttg cccttcttag 540 accagggctg gcaagttcat gtgccttttc tagagagggc agttctagca cagggcccac 600 tagctgttgg caggtatgag tatgggctca gggtngctag tttaggtctt tgtatatgtt 660 tgagtgttta gatgttggtg actaatttgc agtgttgaaa gccacagtat ggacgagatg 720 aggggtctgc aggctcagct tgcctctt 748 13 1098 DNA Homo sapiens misc_feature Incyte ID No 346813.3.j 13 cacaaaacca ttgaagtttn caacacccta acccagccac cttactnctg gtaacagaga 60 gcccagttaa acataactgt ttagaggtgc tggactnagt ttattntagt aggnctaacc 120 tccgagacca cccttaaaca tcagtagact gggagctgta cgtggatggg agcggctttg 180 ccaacccctg caaagtgact ctgaagaagg agacaagccc tgctccagtc acacccagaa 240 gctgactggt ccacgcacag gcgaagcatg aggaaactca ttgcgggact cattttcctt 300 aaaatttgga cttgtacagt aaggacttca actgaccttc ctcagattga gaactgtttc 360 cagtatatac atcaagtcac tgaggtagga caaaaattgc tacagtccta ttattttatg 420 gttattataa gtgtaccagg actctaaaag aaacttgttt gtataatgct atccaaggta 480 tgtagcccag ggaataacca acctgatgtg tgttatgacc cattttaagc ctcccgtgat 540 cacagttttt aaaataaaat taaggactgg tccttttcta ggtgacacaa gtaaggtaat 600 agctagaatg gaaaaaagag gggcccccaa aaatgtaacc ttaaaatttg gtgcttgtgc 660 cgctattgat agtaagcagc atggaatagg atgcggttct ctaaattgga aaaaaaaagt 720 gacacagtaa aaaaaaaata agtgtatctg tcaagaattg tatttatgtg agatgtgtca 780 atactggtct tgtgtcattt gggctactta aaaagaagat aaaaaagatc ctgtttggcg 840 gcttagttgt cttgggcaaa aactgtataa tggtaccaca aaaagttaca tggtggagtt 900 ccaattacac agaaagaaat ccattcagta aatttccaaa nttncanact gtttgggccc 960 acccagaact ccaccgggac tgganagccc ccaccgggtt atacgcagag cttntgctaa 1020 gctccctgat cagtggacag gnagctgtgt aattggcacc attaagccat ctttcttctt 1080 atgcccataa aaacaggt 1098 14 539 DNA Homo sapiens misc_feature Incyte ID No 006861.1.j 14 tttgctgttt gatattggaa tacactctta aatcaatgtg gttatgccac acatcatttt 60 aatgtgaatt tctcacttta tgcttttttg cgactgagtt attacttgcc gtttaagttt 120 attttagact gtggaaaaga cgttagacaa aaagcaaatt cgagtgattt tcttattcga 180 gttaagaatg ggttgtaaag cagtggagac aactcggcaa catcagcacc acattgggcc 240 caggagccgc tgggaaccac taaacgagca tacagtgcag tgctgggtca agaagtttta 300 caggctggga ttagaggcgt gagcactgtg ccctactgaa cgctgtttct agtgataact 360 tgctgctcta tttttagcaa gtttactata tttatttact ttattcaacc agcaattact 420 gagaatctgc tataggcagg ttctgggaac acaggaaaca aagcaaacaa cagaaataag 480 aattggtctt ttcctggtag gaatttaaaa tctaatggga gcagcagcag tctctttcc 539 15 863 DNA Homo sapiens misc_feature Incyte ID No 028008.3.j 15 gggatctggc ctttgtaccc ctaggctgga gttaggtccg gagtttttat cttcatcttt 60 agtactgtac tgtttctcag gttcattgag gaggcactga gaacaaatgg gatatttttt 120 ccatgatgag ggaaaaaacc ccaaccctga gagagattca gtgaggatag cgggagacgg 180 aaaagttaga cctcagagca cttctctgcc agctcttcta ttcttttttc aagtcccttg 240 tgggcaagga tgtggtcgtg gaactaaaga atgacctgag catctgtgga accctccatt 300 ctgtggatca gtatctcaac atcaaactaa ctgacatcag tgtcacagac cctgagaaat 360 accctcacat gttatcagtg aagaactgct tcattcgggg ctcagtggtc cgatacgtgc 420 agctgccagc agatgaggtc gacacacagt tgctacagga tgcggcaagg aaggaagccc 480 tgcagcagaa acagtgatgg ctcctcctcc tcttcccctc cntctttcat tggtgaccca 540 taaccccaag tcccagccca gaacccctaa cccccaatac ttgaaggggt tttgtttttt 600 tactaatgat ggttttgtgg gtttttttta agggatgagt ggatgagagg agtaataggg 660 aacagctatc ctctcttgag aaggggagga taagtaggct gggaaacttc aaagccttcc 720 cagtccccag cacctgcctt tctcactact tctctggaga tggtaggaga gtttcctagg 780 tctttccagg gcagcatgtg attcatttgg ggatggaagg aatctgtccc gcatcgggaa 840 taaaatttat gatgcaaaaa aaa 863 16 2600 DNA Homo sapiens misc_feature Incyte ID No 346078.5.j 16 cctgaggact cagcgaaggg tgggcgccgc cgaggcctcc tgccgctggc gggtttccgc 60 ggagtgccgc ccggctccgc tctgccgccg gcgcggctca tgggcagagt cggccgggcg 120 ggccggcatt aaactgaaga aaagatgtcc ctgtacgatg acctaggagt ggagaccagt 180 gactcaaaaa cagaaggctg gtccaaaaac ttcaaacttc tgcagtctca gcttcaggtg 240 aagaaggcag ctctcactca ggcaaagagc caaaggacga aacaaagtac agtcctcgcc 300 ccagtcattg acctgaagcg aggtggctcc tcagatgacc ggcaaattgt ggacactcca 360 ccgcatgtag cagctgggct gaaggatcct gttcccagtg ggttttctgc aggggaagtt 420 ctgattccct tagctgacga atatgaccct atgtttccta atgattatga gaaagtagtg 480 aagcgccaaa gagaggaacg acagagacag cgggagctgg aaagacaaaa ggaaatagaa 540 gaaagggaaa aaaggcgtaa agacagacat gaagcaagtg ggtttgcaag gagaccagat 600 ccagattctg atgaagatga agattatgag cgagagagga ggaaaagaag tatgggcgga 660 gtggccattg ccccacccac ttctctggta gagaaagaca aagagttacc ccgagatttt 720 ccttatgaag aggactcaag acctcgatca cagtcttcca aagcagccat tcctccccca 780 gtgtacgagg aacaagacag accgagatct ccaaccggac ctagcaactc cttcctcgct 840 aacatggggg gcacggtggc gcacaagatc atgcagaagt acggcttccg ggagggccag 900 ggtctgggga agcatgagca gggcctgagc actgccttgt cagtggagaa gaccagcaag 960 cgtggcggca agatcatcgt gggcgacgcc acagagaaag gtgtgtcccc agggaagcgt 1020 gtgactagag ggaaaggact ggccccatcc atatcagaca tggccagtct tgatcctcat 1080 gtgtcagcag ggggacaatg aggcgtgtgg ccagagggag agggctggcc ctgccatcac 1140 tagaacacag gccgtcctgt tcatatgatg cactgccact tccgttttgt gaaaccagga 1200 atcctgaggc tcatctttat tttttcagaa cagacgtaga gagatgaagg cttgtggagg 1260 aaaagatggt gagagacttg ggcagaaaat gagtagtcct caggaagaaa tcttggttat 1320 gtgtttagag catgaaggac agagccatat agtgtggcag tgaatatacc tgctatctcc 1380 atctcagagg tcgtctctac ttttcccttt tgccctttca gtatagatgt gatttctgat 1440 tctcttacag attgtttgct ttgcgagatc tgatgttatg ttgcagtctc ttggtaaatg 1500 atgcctagtt ggtgttttat tttcatttaa tttttacagt ctgttctgtg ttgagggaat 1560 tcaggaaaga gacaaacata tgttagcatt ttaatcaggg aattaagttt gagtcagcct 1620 agctgaactt cctttgctaa agaaagaaga aaacttttct ggcagccccg ttcatgcaca 1680 gcttaggata catcacgagc ctgacaggtg agtgccagaa accaacagtt gtcccgactt 1740 gtgaggttat ctgaagtaag gcagccggtg gctggattag taactgcata ttcccctggg 1800 cccgtgacct tgaacgtttg ctccaagtca actcacctat aggaattatc actcacatgc 1860 cctgtcagcc ctttgggaag tgagatgagc aaaaattgca agtaatggtg gaggctcaaa 1920 acatccagat gctattgtaa aaacatgcca aagcaaagca gaggctttta ttgcagataa 1980 ggctgtgttt tcgctcagag accaattgtg tagatgccta ggacataaat ggcggggatc 2040 gctattgaaa ttaaattaat tattgtaagt aggactcagt tctgtaacac atctaatgat 2100 atgctgctca gttctgtaac acatctaatg gtatgttttg atacagatgc atccaagaag 2160 tcagattcaa atccgctgac tgaaatactt aagtgtccta ctaaagtggt cttactaagg 2220 aacatggttg gtgcgggaga ggtggatgaa gacttggaag ttgaaaccaa ggaagaatgt 2280 gaaaaatatg gcaaagttgg aaaatgtgtg atatttgaaa ttcctggtgc ccctgatgat 2340 gaagcagtac ggatattttt agaatttgag agagttgaat cagcaattaa aggttagtgg 2400 tacagctaaa tattaaagaa taaaaaagtt gaatttacag ccttaatctt tacaagtaaa 2460 gttactgttt aattaaagtt aaacctttat cttataggat acctgtatta actgtctttt 2520 gtttgccttt cagcggttgt tgacttgaat gggaggtatt ttggtggacg ggtggtaaaa 2580 gcatgtttct acaatttgga 2600 17 414 DNA Homo sapiens misc_feature Incyte ID No 394637.1.j 17 tggttatgtt atacataatt ttaacttgca tttcttgctt tatgtttttt ttgctaatga 60 cttactactt gctgtttatt ttatatttat tttagactat ggaaatgatg ttagacaaaa 120 agtaaattcg agagattttc ttatttaagc tcacaatggg tcgtaaaaca gcagagacaa 180 cttgcaatat caacatgcat ttggcccagg aactgctaat gaacgtacag tgcagtggtg 240 gttcaagaag ttttgcaaaa gataccagag ccttgaggat gaggagtgta gtggcaggcc 300 actggaagtt gacaacaacc aattgagagc aatcattgaa gcagattgat cctcttacaa 360 ttacatgaga agttgctgaa gaactcaacg taagaactca acgtcaacca ttcc 414 18 1307 DNA Homo sapiens misc_feature Incyte ID No 222429.3 18 gggaaatcca gccctcccaa actcttgcct ttcttgtaag actttctaag cgcatggctt 60 tgtcgtaaga cttctcgtgg ccatgtgtct caccctaccg ttcgtctcac caatgaacca 120 gagctgggat accagcaaaa aggacccaaa agactgtttc accacaattg aagaggtcgt 180 ggaccatccc ccaaaatgaa tcccaacact ggaagaccaa gagggttgac gtttgctatc 240 ttgaaagctg cagcccccgt agagaagatc ctagagcaga aggagcacag gctgggctgc 300 catagcatgg acccccaaaa agccactgtc atgaagaaat atcctgtgaa gaaaatcttt 360 gcagggcacc tgaactccca aagccactga ggagaagaat tgcaaccttg gccaatggac 420 ctgatcggtt ttggttatgc agccctcgtg acatttggaa gcatttttgg atataagcgg 480 agaggtggtg ttccgtcttt gattgctggt ctttttgttg gatgtttggc cggctatgga 540 gcttaccgtg tctccaatga caaacgagat gtaaaagtgt cactgtttac agctttcttc 600 ctggctacca taatgggtgt gagatttaag aggtccaaga aaataatgcc tgctggtttg 660 gttgcaggtt taagcctcat gatgatcctg agacttgtct tgttgctgct ctgagcatct 720 ggaggaacag aaaactaagt tcatgtcatc ctgctgtaat gggcagagca tatttttttt 780 gtatttaaaa gataaacttc aatatggaat gctagaaaca caaatagcac tgtcacctct 840 aatatgaaca ttagtttgag gtagtttttt tctaaaacaa aaattttaac tgttttctaa 900 ttgtcaagca ctattttcat taaaagtgtc taatgaatca tgatatactc ttccatttgt 960 tgtgtctatt ttttatatat ttggtatttt ttgaaaattc caaatactca tgtctcaagt 1020 aagcttaaac tacaacttgt cacataaagg aagtcttaag tggagttcac agaatgataa 1080 tgtatctatt tgtcatttgt gttatatttg aaattattag aaattatgct ttttccattt 1140 taattgtatt gctgccagtg ctattttttt ctttaaaaaa ttttattctt agcacactgt 1200 tatgtcctaa ctgaatgtat tcagtattca aataaaagac aaatgacaaa tagatacatt 1260 atcattctgt gaactccact taagacttcc tttatgtgac gtcgacg 1307 19 1406 DNA Homo sapiens misc_feature Incyte ID No 366739.2 19 tgctgccagc gagagccgcg ggagagtgtg cagccgagtc actactgcct gcctgcctgc 60 ctgctacggt gagtgtggcc cccacaatgg gatggcgcag ggcaggaggg ccatgggttc 120 ccccacccca gactaagggg gcactagggg aggggccgag tcatgtgaag agggagaccc 180 tctcagacag tcgaatgtgc tggtcccact aaggaaacca cctcaccctc tccaacttcc 240 tgcctgaaaa tgggccctgg agctcgcaga cagggcagga ttgtgcaggg aaggcctgag 300 atgtgcttct ncccaccccc taccccactc cctccccttc ggatcttaac actgggcact 360 cacacaccca ccccatgctc ctctccaggc tcagcagcag gtactgtacc caaccatggg 420 ctcgcaggcc ctgcccccgg ggcccatgca gaccctcatc tttttcgaca tggaggccac 480 tggcttgccc ttctcccagc ccaaggtcac ggagctgtgc ctgcctgcct gtccacagat 540 gtgccctgga gagccccccc acctctcagg ggccacctcc cacagttcct ccaccaccgc 600 gtgtggtaga caagctctcc ctgtgtgtgg ctccggggaa ggcctgcagc cctggcagcc 660 agcgagatca caggtctgag cacagctgtg ctggcagcgc atgggcgtca atgttttgat 720 gacaacctgg ccaacctgct cctagccttc ctgcggcgcc agcaccagcc ctggtgcctg 780 gtggcacaca atggtgaccg ctacgacttc cccctgctcc aagcagagct ggctatgctg 840 ggcctcacca gtgctctgga tggtgccttc tgtgtggata gcatcactgc gctgaaggcc 900 ctggagcgag caagcagccc ctcagaacac ggcccaagga agagctacag cctaggcagc 960 atctacactc gcctgtatgg gcagtcccct ccagactcgc acacggctga gggtgatgtc 1020 ctggccctgc tcagcatctg tcagtggaga ccacaggccc tgctgcggtg ggtggatgct 1080 cacgccaggc ctttcggcac catcaggccc atgtatgggg tcacagcctc tgctaggacc 1140 aagccaagac catctgctgt cacaaccact gcacacctgg ccacaaccag gaacactagt 1200 cccagccttg gagagagcag gggtaccaag gatcttcctc cagtgaagga ccctggagcc 1260 ctatccaggg aggggctgct ggccccactg ggtctgctgg ccatcctgac cttggcagta 1320 gccacactgt atggactatc cctggccaca cctggggagt aggccaagaa ggaaaatctg 1380 acgaataaag acccccgctg ccccat 1406 20 3028 DNA Homo sapiens misc_feature Incyte ID No 474635.6 20 ccccagcccg ccatggcgtc aggcgccgcg gccccgggga ggtggctccc actttaagaa 60 gtgaagtttt gctcccctcc ccctccctgc ccacctcctg cagcctcctg cgccccgccg 120 agctggcgga tggagctgcg cacgggagcg tgggcagcca ggcggtggcg cggaggatgg 180 atggggacag ccgagatggc ggcggcggca aggacgccac cgggtcggag gactacgaga 240 acctgccgac tagcgcctcc gtgtccaccc acatgacagc aggagcgatg gccgggatcc 300 tggagcactc ggtcatgtac ccggtggact cggtgaagac acgaatgcag agtttgagtc 360 cagatcccaa agcccagtac acaagtatct acggagccct caagaaaatc atgcggaccg 420 aaggcttctg gaggcccttg cgaggcgtca acgtcatgat catgggtgca gggccagccc 480 atgccatgta ttttgcctgc tatgaaaaca tgaaaaggac tttaaatgac gttttccacc 540 accaaggaaa cagccaccta gccaacggta ttttgaaagc gtttgtctgg agttagaaag 600 ttctcttctt caacacgtcc ctccccaggg tgttcctccc tgtgacccag ccgcctcgac 660 ttcggcccgc ttgctcacga ataaagaact cagagttgtg tgtgcaatgc acacccagac 720 acacgcacgc acacacacgc gcgcgcacac acatgctttt ttctgttccc ctccgctttc 780 tgaagcctgg ggagaaatca gtgacagagg tgttttggtt ttattgttat gtgggttttc 840 ttttgtattt tttttgtttg ttttgttttt aaacattcaa aagcaattaa tgatcagaca 900 taggagaaac cctgaataga aacaaaactt ttgaatgctg gattcaaaaa aaaaaaaaag 960 ttatctggac agcttctttg agactattta aaaactggta caacaggtct ctacaacgcc 1020 aagatctaac taagctttaa aaggtcaaga agttttatgg ctgacaaagg actcgcgcaa 1080 cgcagaaggc ctttcccacc ttaagcttcc ggggatctgg gaattttacc cccattctct 1140 tctgtttgtc tgagtctcat ctctctgcaa gcaagggctg aaatcatttt gtttggttgt 1200 tttgagggag agaggcgggg tgggggggtg caaatctgcc agcagctctt acgtaaggca 1260 tgttttattg gggagggctg agcttttatt ttctcctctc cagtggggtt ggcttttatt 1320 gtttcttgtt tgggtttgga atggaaatat ggatagcagc ataaagtact tttattttga 1380 caaaattcat ttttttcaac aatggagaca tagatttgac ccacaataac ttctccccct 1440 ctctttttac tctgctcaaa aagcatctct cctcccatta cccaaccttg gtcataagtg 1500 tgcctggctg gtttgcagat atttgttctg ctttgtaaaa attggccatt agtgcattta 1560 ttgagatgat ctctaaagag ctatgccctg acctacccct gattctatga cattggggcc 1620 cttcttttgc tgaaactgcc ttacgtaatg gttttactcc ttgaaagaga tttgacggaa 1680 tccattttat gccaagtgct gccctgcact gtttctgcaa tatgtggtgt atgctgtggt 1740 gatcttgctg ggaatgatta taagtgtgtg tgtggtgggg gagtgggtat tacatgcatt 1800 gctgaagagt catcctggtg ttcctcattc ctcccacctt cccgtggtca ttttaattac 1860 ggggcagtgt caccgcaaag ggaggaaact caaagccgaa agcaaaattc caggcctgat 1920 tctggctttt gaggttcctg gttcttgaag ccaggcctga cccgactctc agatggggtc 1980 agtcccgtcg ctttgcagac tgaccctgga aatctacaaa atgcagattt tcctgatttc 2040 ctcttctctt gcccagtttt ttnntgtntn tttttttnna aaagcctgga ttgtaaccag 2100 attttctttt ttcccccttc tcagctgtag atatgatatc tcctttcagg gccccagctt 2160 aagggcaaag tgagttaatg tgtagacaaa ggcgagggac aagagagagt taacatctag 2220 acagtggaaa aagccatggt gtgtggtttc tgggaaccac caacacttgc aggtttagct 2280 ttttcccagg gttgactaca agaaagaaaa ccatgttttt gcaagattaa aatgtggttg 2340 agtgtgccta aattaaccat ccccattttt atcatatttc caccatcact tcagggtttt 2400 aagagtcagt gctcacctgg gcggagctgg tagtacattt tgcttcttag aaagctaagt 2460 cctgggttcc gtctgatttt aggttccagg aacttcctga gaacacccga tcgcagaggg 2520 taattttctg gagtttgttt tgcagggata gctgggagta tggccaccct gctccacgat 2580 gcggtaatga atccagcaga agtggtgaag cagcgcttgc agatgtacaa ctcgcagcac 2640 cggtcagcaa tcagctgcat ccggacggtg tggaggaccg aggggttggg ggccttctac 2700 cggagctaca ccacgcagct gaccatgaac atccccttcc agtccatcca cttcattttt 2760 ttttgcaggg tgctgcctat gggccctctg ctccccaatg ccttagagag aggaggggag 2820 ccacggccgc tcaccggaag gctgtgtgcg gggacatccg aggtggtggt ggacaggaag 2880 gacttgggaa ggggagcgag aaattgcttt ttctcttcct ccttgggcag aatgtagctt 2940 ttctgcttca ctgtggcagc ctcctccctg gatccttaga tcccagagga gggaagaaaa 3000 tttgcagtga ctgaaaacag taaaaaaa 3028 21 537 DNA Homo sapiens misc_feature Incyte ID No 228470.1.j 21 cggagaagtc atactctctc acaccctcgg ctttcttgtt gtgtccttca gcaaaacagt 60 ggatttaaat ctccttgcac aagcttgaga gcaacacaat ctatcaggan aganagaaag 120 aaaaaaaccg aacctgacaa aaaagaagaa aaagaagang aanaaaaatc atgaaaacca 180 tccagccaaa aatgcacaat tctatctctt gggcaatctt cacggggctg gctgctctgt 240 gtctcttcca aggagtgccc gtgcgcaggg aagatgccac cttccccaaa gctatggaca 300 acgtgacggt ccggcagggg gagagcgcca ccctcaggtg cactattgac aaccgggtca 360 cccgggtggc ctggctaaac cgcagcacca tcctctatgc tgggaatgac aagtggtgcc 420 tggatcctcg cgtggtcctt ctgagcaaca cccaaacgca ttacagcatc gagatccaga 480 acgtggatgt gtatgacgag ggcccttaca cctgctcggt gcagacagac aaccacc 537 22 3080 DNA Homo sapiens misc_feature Incyte ID No 407090.5.j 22 gcggcgctgg ctttaggtga acgacgtggt gaggagtggg tttcgggcat gagaagtcac 60 agggccgttt cctagtctct cttcacttct ttgggtcttc tcagagaaag aaggctgccg 120 tgggtaggct gggggcggag actatcggga agagaaaatt acttttccca ctgaaacaca 180 cccaagtata tgcccagcct tcatgaaagt gaacagagaa acgaagcgcc tttatgtggg 240 tggccttagc caggacattt ctgaggcaga cctacaaaat cagttcagca gatttggaga 300 agtttcggat gtggagatca tcacacggaa agatgaccaa ggaaacccac agaaagtttt 360 tgcatatatc aacatcagtg tagcagaagc ggacctgaaa aaatgtatgt ctgttttaaa 420 taaaacaaaa tggaaaggtg gaacattaca aattcaacta gcaaaagaaa gctttctgca 480 cagattggcc caagagagag aagcagcaaa agctaagaaa gaagaatcaa caacaggtaa 540 cgccaacttg ttagaaaaga caggaggagt ggatttccat atgaaagctg tgccagggac 600 agaagtgcca gggcataaga attgggttgt gagcaaattt ggaagagtct tacctgttct 660 tcaccttaaa aatcaacata aacgtaaaat catcaaatat gatccctcaa aatactgcca 720 caacctgaag aagatagggg aggatttctc aaacaccatt cctatatcca gcctgacttg 780 ggaattagaa ggagggaatg accctatgag taagaaacgg cgaggagagt tctctgactt 840 tcatggccct cccaagaaga taataaaagt gcagaaggat gagagttccc actgggtctc 900 tggccatgag tacaaggccc aggagggtaa tagagagacc acccttaaca cagcaacagg 960 ctgcacaaaa aagaacttgt gattccatta ctccttctaa atcatctcct gtacctgttt 1020 ctgatactca gaaacttaaa aatctacctt ttaagacttc tggcttggaa actgccaaga 1080 agagaaacag catttctgat gatgatactg attctgaaga tgaattgaga atgatgattg 1140 cgaaagagga aaacttacag agaactacac aaccctcaat aaatgaatct gaaagtgatc 1200 cttttgaagt tgtaagggat gatttcaaat caggcgttca caaactgcat tctttaatag 1260 gtttaggtat caaaaatcgt gtctcttgcc atgatagtga tgatgatatt atgagaaatg 1320 atcgtgagta tgactcagga gatacagatg aaattattgc gatgaaaaaa aatgttgcta 1380 aggtcaaaaa cagtacagaa ttttcacaaa tggaaaaatc tacgaagaaa acttctttca 1440 aaaatagaga aaactgtgag ctttctgatc actgtattaa actacaaaaa agaaaaagca 1500 atgtagagtc agccctcagt catggattaa agtctcttaa tcgtaaatct ccctctcact 1560 ccagtaggca gtgaagatgc tgattctgca tcagaattag ctgactctga aggaggtgag 1620 gagtataatg ccatgatgaa aaactgcctt cgtgtgaatc tcactttagc tgatttggaa 1680 caattggctg gcagtgatct gaaggttcca aatgaagata ctaagagtga tggaccagaa 1740 accaccaccc aatgcaagtt tgacagatgc tccaagagcc ccaagactcc cactggcctc 1800 cgcagaggcc gacagtgtat tcgtcctgcg gagattgtgg cttccctgtt agaaggagag 1860 gagaacacct gtggcaaaca gaaaccaaag gaaaacaatt taaagccaaa atttcaggct 1920 ttcaagggag taggctgtct atatgaaaag gagtcaatga aaaaatcctt gaaagacagt 1980 gttgcctcta acaataaaga tcagaattcc atgaaacatg aggatcccag tatcatatcc 2040 atggaagatg ggtccccata tgttaatggc tcattaggtg aagtgactcc atgccaacat 2100 gcaaagaagg cgaatggccc aaactatatt cagcctcaaa aaagacagac cacttttgaa 2160 agccaggatc gcaaggcagt gtcccctagc agttctgaaa agagaagtaa gaatcctatt 2220 tctaggccat tagaaggtaa gaagtcctta agtcttagtg caaagactca caacataggc 2280 tttgacaaag acagctgcca tagtaccaca aagacagaag cttcacagga agagcggtct 2340 gattcaagcg gcctcacatc tctcaagaaa tcaccaaagg tctcatccaa ggacactcgg 2400 gaaatcaaaa ctgatttctc actttctatt agtaattcgt cagatgtgag tgctaaagat 2460 aagcatgctg aagacaatga gaagcgtttg gcagccttgg aagcgaggca aaaagcaaaa 2520 gaagtgcaga agaagctggt gcataatgct ctggcaaatt tggatggtca tccagaggat 2580 aagccaacgc acatcatctt cggttctgac agtgaatgtg aaacagagga gacatcgact 2640 caggagcaga gccatccagg agaggaatgg gtgaaagagt ctatgggtaa aacatcaggg 2700 aagctgtttg atagcagtga tgatgacgaa tctgattctg aagatgacag taataggttc 2760 aaaattaaac ctcagtttga gggcagagct ggacagaagc tcatggattt acagtcgcac 2820 tttggcaccg atgacagatt ccgcatggac tctcgatttc tagaaactga cagtgaagag 2880 gaacaggaag aggtaaatga aaagaaaact gctgaggaag aagagnttgc tgaagaanaa 2940 nagaaagccc tgaatgttgt acaaagtgtt ttgcaaatca acttaagcaa ttctacaaac 3000 agaggatnag tagctgctaa gaaatttaag gacatcatac attatgatcc ancgaagcaa 3060 gaccatgcca cttacgaaag 3080 23 426 DNA Homo sapiens misc_feature Incyte ID No 068194.1.j 23 cccaagtccc tagaagaagc caccccatcc aaggagggtg acatcctaaa gcctgaagaa 60 gaaacaatgg agttcccgga gggggacaag gtgaaagtga tcctgagcaa ggaggacttt 120 gaggcatcac tgaaggaggc cggggagagg ctggtggctg tggacttctc ggccacgtgg 180 tgtgggccct gcaggaccat cagaccattc ttccatgccc tgtctgtgaa gcatgaggat 240 gtggtgttcc tggaggtgga cgctgacaac tgtgaggagg tggtgagaga gtgtgccatc 300 atgtgtgtcc caacctttca gttttatnaa aaagaagaaa aggtggatga actttgcggc 360 gcccttaagg aaaaacttga agcagtcatt gcagaattaa agntaaacat gtattctgaa 420 aacaaa 426 24 3219 DNA Homo sapiens misc_feature Incyte ID No 411449.2 24 ggaaagggaa acaaccacat aaacgcaaga aaaaatccag gaaaaagtct ctcaaaaaac 60 ctgctttatt cttagaggca gaaagtaaca cttcacattc agatgattca gcatccagca 120 gttctgagga aagtgaggaa agagacacta agaaaaccaa aaggaaaaag agagagaaaa 180 aagcccatac ctctgtagcc aacaatgaaa tacaggagag gacaaacaaa cgcacaaatt 240 ggaaagtagc tacagatgaa aggtctgctg agagctcaga ggatgactaa atgggaaaca 300 cttttgtttt ccacatgact gtggatattt acagttctta ctccttgtgg ttttgccagt 360 gactcttgtt cagcacgggg cctgaggtca gagctgtctt gtgccatctg tatgttctga 420 cagacgtctt gtcttctatt ttggcgttaa gcttgatccc cttttcttgt taaaagggaa 480 tctggtattt tgttatgaag gtttcttgaa gagatttttt tttttgcaat taattacgtt 540 tagtgtagag tgcatataca gcaaattaaa ggacccagaa agctggatcc aatagtgacc 600 tgggtacacc aatcggaata ttgaatttgg ggaagtcaag ggctgggatc caagaggtgg 660 attggaacta atgccatgta ggatggtatg acaaggcaac actgtattgc tctctgttta 720 tatagcaggt gtcacaacta acttgtcttt agccttggtg ctttgatcct tctatatttt 780 gaccccacag gtgtggtccg gtttacttaa tcaggacatg ggcctaagaa caaacctttt 840 cccttcatga taacatccat agacaactta ttagaaggga ctagagtttt tgcaaatttc 900 cctgctggat ggggcctata gctatactta gtatatgcct aaacatggta attggatagt 960 aaatggtttt ctagttccat tgctgtatat ttgcctaaat ggacttgtgt tcaaattatt 1020 tcttcaattg tcatagataa tcctgtacca aatggggaag aattaggaaa taatcatgtt 1080 gtctaatggt actctggatt cagggcagca actgccattt aaatgttgtc ttgttcattt 1140 ctaaatctgt tcatgaagtt taggttttcc ctgaaactaa gttgaattat ttccaaaatg 1200 aaacaggctt ctcagggaca tatccacttc ttcccagtct gcctttggat taaagcacca 1260 agcagagacc acattaattc cctttgctat actgtgatcc ttagtatgtt aattcttaag 1320 aaaccaacat atcactgaaa gaaggctggc agaacgcaag tgcatttttt cactgtggga 1380 agaaagatca agtgacgtat tattttttcc tggttgtcac ttaatgggct gagtaaaaag 1440 cttgaaaact cagactttcg gtcttggttc tgccactcat tggttatgag gaggcccaga 1500 gcaggtaagt tcaccttcct ggccttactt tcctgatgtg taatacggaa ttacttcaca 1560 gtagcatgac agtataagac accagcagta gatacaacta tgatgacatt ccatgagttg 1620 gtatttttag ttctaactgc taaatttgtt ctctttacgg gacagatttc taataaagtg 1680 cttggtctta aaatacatgg ttggacagag gtgccctatc ccttaactat gagcaggtgc 1740 taccttttgg gatatttatt ttaaatttta atactttggt actcaattgt cagtgttcca 1800 tggtgtgtat ttttattttt gggattagtg ggggtctaaa gggagaagaa tagtctctaa 1860 ttactacctc ttaacctaaa gcaattattt tgttcctgga gcaagttaaa tctttgttgg 1920 aaggagcttt ggccatatat tttttagcat gcattgtttc tgtgccctga aagtacctga 1980 aaggttttaa gcacagactc aggaaaatgt gccagtagaa caggccatct ccaggaaatt 2040 ggctctattt gggtcctgac cttcccttcc tcccaagtta gcaggcttgt tcttttgcaa 2100 ggaatacaca tcttgccttt tttttttttt ttgccatgtt ttccttttct tggtcatgta 2160 taagcaataa agctgttttt tgttcttcat ctttcttaac cccaaatttt cttctatgcc 2220 ttaggcttcg atggttcttc caaccccctt aatatggctt agggtggttt ttcaaaacct 2280 acaatccccc atttgcacta ctggccatgg aacatttatt tctagtgttc ctgccaatca 2340 gagatctcta tattaaattc taaaatggga ttaaaagaag agttggagaa ttcacactta 2400 ttgagtaact gatgtcatac aacctggaat ttctgaattc caaataaata aatttcactc 2460 tttgaacatt tcatctttta ctttttagca ccaacagact tgataacagc ctgatgctga 2520 tctgacaatg ggttgatagc cttcccccac tgacccttaa atctgcttag taacaagtcc 2580 tttgcttctg tcattctcct gggggatggc ctactgccct cctttctgta caatctgggc 2640 aaaccgactg gtgatggcaa gagtggtgtc aatgaagcgg tctacacagc tggagagaca 2700 attttcagtg cgagagtcta ggcgattccc tggcttctcc acacatttat cccaacataa 2760 ctccatgaag tgatgcacta tttgtgaggc tgggtactaa gaaatcagtt ctctctaagg 2820 tcctcaagga tagctgtcat cacctcccat ttaagaggcg tgattatgta gtccaaggtc 2880 atgtagccag caagaagtca ggccgcgtta gaaccatgtc cgaagggctc caaacccttg 2940 ttctacatcc atagtctaca gcgactactt cagagtccac cttcctccga taatgttcta 3000 gtcgttttca aatacattgt cgcatatgat cctcacaatc cagtgaggca gtggggtgac 3060 ggcgaaacca aaacccacag tggaatgnag tatcttttct acgggcacgt ggcctgtgca 3120 gtaaactgcg ccttctgctg ctcggcggcc accaggcgct gcaactccgc ttcatcggct 3180 tcgcccagct ccgccattgt tcgcctgcag gctcgccac 3219 25 445 DNA Homo sapiens misc_feature Incyte ID No 018549.2 25 tgacttttgg gagagctgac cttttgtgac tttngggaga gctgccaaaa gtgaaactta 60 gtgcctcaga caagcagggg caagtctgct aaggaagctg tggccagaag cacagatcag 120 aaacacgatg gctctgttaa cagccgaaac attccgctta cagtttaaca acaagcgcct 180 cctcagaagg ccttactacc cgaggaaggc cctcttgtgt taccagctga cgccgcagaa 240 tggctccacg cccaccagag gctactttga aaacaagaaa aagtgccatg cagaaatttg 300 ctttattaac gagatcaagt ccatgggact ggacgaaacg catgcttacc aagtcacctg 360 ttacctcacg tggagcccct gctcctcctg tgcctgggag ctggttgact tcatcaangc 420 tcacgaccat ctgaacctgg gcatc 445 26 1657 DNA Homo sapiens misc_feature Incyte ID No 236043.3 26 ccggnccggg ctcctcctgc tgctgggaca gtgctctagt agaacagaca gacctactga 60 cacaggggag gtgagaaggg aggtgaccac caggactggc tctgtgagta ccacacagtg 120 gggagggggt gggggccacc atgtcatcat atcagaagga actggagaaa tacagagaca 180 tagatgaaga tgagatccta aggaccttga gccccgagga gctagagcag ctggactgcg 240 aactacagga gatggatcct gagaacatgc tcctgccagc tggactaaga caacgtgacc 300 agacaaagaa gagcccaacg gggccactgg accgagaggc ccttttgcag tacttggagc 360 aacaggcact agaagtcaaa gagcgtgatg acttggtgcc cttcacaggc gagaagaagg 420 ggaaacccta tattcagccc aagagggaaa tcccagcaga ggagcagatc accctggagc 480 ctgagctgga ggaggcactg gcacatgcca cagatgctga aatgtgtgac attgcagcaa 540 ttctggacat gtacacactg atgagtaaca agcaatacta tgatgccctc tgcagtggag 600 aaatctgcaa cactgaaggc attagcagtg tggtacagcc tgacaagtat aagccagtgc 660 cggatgaacc cccaaatccc acaaacattg aggagatact aaagagggtc cgaagcaatg 720 acaaggagct ggaggaggtg aacttgaata atatacagga catcccaata cccatgctaa 780 gtgagctgtg tgaggcaatg aaggcaaata cctatgtgcg gagcttcagt ctggtagcca 840 cgaggagtgg tgaccccatt gccaatgcag tggctgacat gttgcgtgag aatcgtagcc 900 tccagagcct aaacatcgaa tccaacttca ttagcagcac aggactcatg gctgtgctga 960 aggcagttcg ggaaaatgcc acactcactg agctccgtgt agacaatcag cgccagtggc 1020 ctggtgatgc agtggagatg gagatggcca ccgtgctaga gcagtgtccc tctattgtcc 1080 gctttggcta ccactttaca cagcaggggc cacgagctcg ggcagcccag gccatgaccc 1140 gaaacaatga actacgtgag taactgcaga catgatgtgt ggagtggtca gggaagtgca 1200 gaaattggtg gatcctcctg aaagcagacc taatgactaa cagcccaggg tgctaccaaa 1260 gagctattca tatgagaatt tcaaatccca agagtgatca gaaagtaaac agaaaactcc 1320 ccctgcccca aatatggacc agtagagagg tagaaaggat gccagagata atcatacttg 1380 tttagaggta tcgtaatttt atttgtggtg tggtttcttg ttttgttttg ttaatgtggg 1440 atgggcctgt aaggtggcct aagacactac caatttatga gtttggctaa gggactggaa 1500 aggagaagag tgcctttgca gaaagcagga gctggaacaa acacttatgt ttaatattgc 1560 tcctttacag gtcgccagca aaagaagaga taacactgca tttcccttta ccaactagcg 1620 ctgggagcac tggtcactta aatcctcatc tgtcctc 1657 27 1041 DNA Homo sapiens misc_feature Incyte ID No 445433.2 27 ttcttcttta attagaagct taaagagaag tttgcagaat gtactcataa gtggatggga 60 taatactgtt aagttctgat attctgatat tgtttgaaat actgttaaga atttcacatt 120 tggtaagtat tttttatatc agtattaaaa tagtaatttg gtttattaca attttataca 180 tagaatttgc cagttacttt ctgactacaa agaaaaacag atactaaaag tctcttctga 240 aaacagcaat ccagaacaag acttaaagct gacatcagag gaagagtcac aaaggcttaa 300 aggaagtgaa aatagccagc cagaggaaat gtctcaagaa ccagaaataa ataagggtgg 360 tgatagaaag gttgaagaag aaatgaagaa gcacggaagt actcatatgg gattcccaga 420 aaacctgcct aacggtgcca ctgctgacaa tggtgatgat ggattaattc caccaaggaa 480 aagcagaaca cctgaaagcc agcaatttcc tgacactgag aatgaacagt atcacaggga 540 cttttctggc catcccaact ttcccacgac ccttcccatc aaacagtgat gaacaaaatg 600 atactcagaa gcaactttct gaagaacaga acactggaat attacaagat gagattctga 660 ttcatgaaga aaagcagata gaagtggctg aaaatgaatt ctgagctttc tcttagttat 720 aagaaagaaa aagacctctt gcatgaaaat agtacgttgc aggaagaaat tgtcatgcta 780 agactggaac tagacataat gaaacatcag agccagctaa gagaaaagaa atatttggag 840 gaaattgaaa gtgtggaaaa aaagaatgat gatcttttaa agggtctaca actgaatgag 900 ctcaccatgg gatgatgata ctgccgtgct cgtcattgac aacggctctg gcacgtgcaa 960 ggccggcttt gcaggtgacg atgccccccg ggctgtcttc ccttccatcg tgggggtgcc 1020 cccaggcacc agagcatgat g 1041 28 2113 DNA Homo sapiens misc_feature Incyte ID No 344630.7.j 28 gcagtgcggc cgtcatggcg tcgcccttca gcggggcgct gcagctgacg gacctggatg 60 acttcatcgg gccgtctcag gagtgcatca agcctgtcaa agtggaaaaa agggcgggaa 120 gtggcgttgg ccaagattcg cattgaagat gacgggagct acttccaaat taaccaagac 180 ggcgggaccc ggaggctgga gaaggccaag gtctcgctaa acgactgcct ggcgtgcagc 240 ggctgcatca cctccgcaga gaccgtgctt atcacccagc agagccacga ggagctgaag 300 aaggttctag atgctaacaa gatggcggca cccagtcagc agaggctggt tgtagtttcg 360 gttctcacca cagtctagag catcgctggc tgcacggttt cagctgaatc ctacagatac 420 tgccaggaaa ttaacctcat tctttaaaaa aataggggtg cacttcgtct tcgacaccgc 480 cttctcaagg cacttcagcc tcctgggaga gccagcgaga gtttgtgcgg cgattccgag 540 gacaggccga ctgcagacag gcgctgcccc tgctggcctc tgcctgccca ggctggatct 600 gctatgccga gaagactcac ggcagcttca tcctccccca catcagcacc gcccggtccc 660 cgcagcaggt catgggctcc ctggtcaagg acttcttcgc ccagcagcag cacttgaccc 720 ctgacaagat ctaccacgtc acagtgatgc cctgctatga caaaaagctg gaagcctcca 780 gacccgactt tttcaaccag gagcaccaga cacgggatgt ggactgtgtc ctcacaacag 840 gagaagtttt caggttgctg gaggaagagg gcgtctccct ccccgacctg gaaccagccc 900 ctctggacag cctgtgcagc ggtgcctctg cagaggagcc caccagccat cggggagggg 960 gctcgggggg ctacctggag cacgtgttcc ggcacgcggc ccgagagctc tttggaatcc 1020 atgtggctga ggttacctac aaacccctga ggaacaaaga cttccaggag gtgacactgg 1080 agaaggaggg ccaggtgctg ctgcacttcg caatggcgta cggcttccgc aacatccaga 1140 acctggtgca gaggctcaaa cgagggcgct gcccctacca ctacgtggag gtcatggcct 1200 gcccctcagg ctgcctgaac ggcgggggcc agctccaggc cccagacagg cccagcagag 1260 agctcctcca gcacgtggag agactgtacg gcatggtccg ggctgaggcg cccgaggacg 1320 cgcctggggt tcaggagctg tacacacact ggctgcaggg cacggactcg gagtgtgcag 1380 gtcgcttgct gcatacgcag taccacgccg tggagaaggc cagcactggc ctggtgcatc 1440 cggtggtagg ggctgcagga ccaggactcc caggaggccg tgtccatgtg tgacagcaga 1500 accacatgcc ccaagacccc agggcttccc ccaaaattct gagtgagctg cagggtgtgc 1560 tgggacccga gtaggagcta ggactagcca ggacccgcag ccgcctcgtc acctccagtt 1620 gggtgcctct gggttcccac tggctctgcc caggtggggt ggggtggccc aggcagcaga 1680 aggttccctg aggtcccaga gcctgttccg ttggccctgg gccgaggccc acaggtgctg 1740 cccttgctgc tgctggtcgg gcacccaagt gcgtgagggg cttcagcctg tcccggggtt 1800 gcctgaggca gagcaagacg ggttctcacc cctgacttct ggaggcttcc cttgaagctc 1860 tgtgcaaaag gtgggagaca gagctggacc tgcaggggtg gtcccgccac aaccctgcgt 1920 gtggaccctg gcaggggggg gtgccaggcc cctggaaagc aggggttacc gttacgaggc 1980 tgtggtccgg ggcaagccaa gtacgaagca gcagccatcg cgggctgcat catcccccag 2040 ccaggtcccc accaggcctg tctcccagcg tttgtctaat aaacgcaccc ctcctaaaac 2100 acgcctacga aaa 2113 29 3813 DNA Homo sapiens misc_feature Incyte ID No 257121.2 29 aaatcaaggg agctaaatgg cggggtggat ggaattgcaa gtattgaaag tatacattct 60 gaaatgtgta ctgataagaa ctccattttc tctacaaata cctcttctga caatggatta 120 acttccatca gcaaacaaat tggagacttc atagagtgcc ctttgtgcct tttgcggcat 180 tctaaagaca gatttcctga tataatgact tgtcatcaca gatcttgtgt ggattgctta 240 ccgacaatat ttaaggatag aaatctctga aagcagagtt aatattagtt gcccagaatg 300 tactgaacgg tttaatcccc atgatattcg cttgatatta agtgatgatg tcttgatgga 360 aaaatacgaa gaatttatgc ttagacggtg gcttgttgca gatcctgatt gtaggtggtg 420 tccagctcca gactgtggat atgctgtgat agcatttgga tgtgccagct gtccaaaatt 480 aacttgtggg cgagagggct gtggaacaga gttttgctac cactgtaaac agatttggca 540 ccccaaccag acctgtgatg ctgctcgaca agagagagcc cagagcttac gtttgagaac 600 tatacgttct tcatccatta gttatagtca agagtctgga gcagcagctg atgatataaa 660 gccatgtcca cgatgtgctg cttatataat aaagatgaat gatgggagct gcaatcacat 720 gacatgtgct gtttgtggtt gtgagttttg ttggttgtgt atgaaagaaa tctcagattt 780 gcattatcta agtccatcag gatgtacttt ttgggggaag aaaccctgga gccgaaagaa 840 gaaaatattg tggcaactgg gaacactggt tggtgctcct gtcggaatcg ctttaatagc 900 tggcattgct attcctgcaa tgattattgg cattcctgtg tatgtgggcc gcaagattca 960 caatcgctat gaaggcaagg atgtttcaaa gcacaaacgg aatttggcca tagcaggtgg 1020 tgtaacgttg tctgtaatcg tgtctccagt agtagctgca gtgactgtag gtatcggtgt 1080 tcctattatg ttagcttatg tctatggcgt agttccaatt tctctttgtc gaagcggagg 1140 ttgtggagtc tcagcaggca atggaaaagg agttaggatt gaatttgatg atgaaaatga 1200 tataaatgtt ggtggaacta acacagctgt agacacaaca tcagtagcag aagcaagaca 1260 caacccaagc ataggggagg gaagtgttgg tgggctgact ggcagtttga gtgcaagtgg 1320 aagccacatg gatcgaatag gagccatccg agacaacctg agtgnaacgg ccagcaccat 1380 ggcactagct ggagccagta taacggggag tctgtcagga agtgccatgg taaactgttt 1440 taacaggttg gaagtacaag cagatgtaca gaaagaacgg tacagtctaa gtggagaatc 1500 tggcacagtc agcttgggaa cagttagtga taatgccagc accaaagcaa tggcaggatc 1560 cattctgaat tcctacatcc cattggacaa agaaggcaac agtatggagg tgcaagtaga 1620 tattgagtca aagccatcca aattcaggca caacagtgga agcagtagtg tggatgatgg 1680 cagtgccacc cgaagtcatg ctggcggttc atccagtggc ttgcctgaag gtaaatctag 1740 tgccaccaag tggtccaaag aagcaacagc agggaaaaaa tcaaaaagtg gtaaactgag 1800 gaaaaagggt aacatgaaga taaatgagac gagagaggac atggatgcac agttgttaga 1860 acaacaaagc acgaactcaa gtgaatttga ggctccatcc ctcagtgaca gtatgccttc 1920 tgtagcagat tctcactcta gtcatttttc tgaatttagt tgttctgacc tagaaagcat 1980 gaaaacttct tgtagtcatg gttccagtga ttatcacacc cgctttgcta ctgttaacat 2040 tcttcctgag gtagaaaatg accgtctgga aaattcccca catcagtgta gcatttctgt 2100 ggttacccaa actgcttcct gttcagaagt ttcacagttg aatcatattg ctgaagaaca 2160 tggtaacaat ggaataaaac ctaatgttga tttatatttt ggcgatgcac taaaagaaac 2220 aaataacaac cactcacatc agacaatgga attaaaagtt gcaattcaga ctgaaattta 2280 ggcccataaa tgctgcagaa taattaccac tgtacaaccg tgtttggagc tggttgaact 2340 acatgtgact acttaagttt caggttacca gcaaaagccg ggtttcatta tcataatgca 2400 gatacatttt ctgtgttcag caaggcattg tgtgtcatgt gggatcttag ttaccaaact 2460 atgaagtgaa ggctttaaaa gtgcattatt ttaaggataa taaatttgaa gagcaaagca 2520 tgttttgtgt gtttgccaca aaacattgct tgaagcacat acttagatag aaattggtct 2580 taatttatat aatcaatata aaatactaat gcaattctac agcattcaaa tgaagaaaac 2640 ttgaggcttt agggataagt ggttagtgat attttattga aaccactaaa gagataagtt 2700 taaaagaact gcataggtta ctctcagtat atgatactct gtaacatttc tatttatatc 2760 ggcataaatt tcattttttt tcttcatatg caatgtggtt atataaagct taatgcagct 2820 catttgctac catttggata cttagacact ttgagcaaga ttgtggcagt ttttgcacaa 2880 ctttgaaata gaaatacctg gtactctatc ttgtttattg ttgatgccat cttagaggaa 2940 aaaatgtaaa ggtaagtaat taagcatatg acagcaacaa ataagataca taaaactaca 3000 aaataaagtc ccattaggtt ataagtatta caaaaaatcc acctttctct aaggggaagt 3060 ttgtacccca ttgattcttg gtgcctttgg gatcgactgg gttttaatgg cctagttatt 3120 tgaggatttt gctgtgttgt tttccatgtc ttctctggtc accttggatt atatataaaa 3180 atacaggaaa tagataaaca tgaatgtgat taataatgct gaaaaagtat tagcctacca 3240 aagacacact caggctttag tgaataactt tacataacct cagtttttaa cacatgcata 3300 tcttctccaa ccatgaaatc aaagcacggt gcagaacttg taccaagtac aaaaggtcca 3360 tgtatgatta gcattatttt cttttgcttt tgtttatgga caatgttcag ctgacataag 3420 cagaagttgg ccaaaatact gcctgtactg ttaatttcct gtataattca cttaaataaa 3480 agcaggttaa cctcaatgat agcagttaaa atgttctatc ttatgtattt cttttaagta 3540 ttaccattat ggtgctactg agcgttttct tttggtaaaa agaaaaatgc catgggctgc 3600 agtcttcttc catcactttt ccctaccagg tccattaata tgcttataac actagtgcca 3660 gttattttat ttgataatgc ttatggtatt tgtatatttg tttaagtgaa ttatacagga 3720 aattaacagt acaggcagta ttttggccaa cttctgctta tgtcagctga acattgtcca 3780 taaacaaaag caaaagaaaa taatgcgtcg acg 3813 30 882 DNA Homo sapiens misc_feature Incyte ID No 243794.1.j 30 ggcccaaact gagttgcgtt gcctcttctt gcaaatgaac ttgctccgta aaattgagaa 60 cctggaacct ctgcagaaac tggatgctct taacctcagc aacaattaca tcaagaccat 120 tgaaaacctc tcctgcctcc cagtcctgaa cacattgcag atggcccaca atcacctgga 180 gaccgtggag gacattcagc atctacaaga gtgtttgagg ctttgtgtcc ttgacctttc 240 gcacaacaag ctgagtgatc cggaaatatg gcctcaatat gtgccgccag tgtttccgtc 300 agtacgcgaa ggatatcggt ttcattaaga aagacctgag ctgtcttcct tggcactgcc 360 tatggaggtg acacccatct cctccatcat ggccatcctg agaccgctcg cgaagcccaa 420 gatcatcaaa aagagcacca agttcactgg gaaccagtca gactgatatg tcaaaattaa 480 gggtaactgg tggaaacaca gaggtattga caacagggtt catagaaggt ttgagggcca 540 gatctatgcc caacattggt tatgggagaa acaaaaagac aaagcacata ctgcccagtg 600 gcttctggaa gttcctggtc cacaacgtta aggagctgga agtactgctg gtgagcaaca 660 aatcttactg tgttgagatc actcatgatg tttcttccaa gaactgcaaa gccatcttgg 720 aaagagcagc ccaggtggtc atcagagtca ccaatgccaa tgccagcctg cacagtgcag 780 aaagtgaata gacagtgaat gtgtttgttt tattggggtt taaataaaac caataaaact 840 gtaaaagcag cggcaacaaa aaccagaaaa aaaaagtcga cg 882 31 514 DNA Homo sapiens misc_feature Incyte ID No 442085.1.j 31 ctcgttcctg tcgcgcagca cggacctcca cttccacatc tcccccggcg tcggcgcggt 60 cagttgaacc atggcggact ccaaggccac ctcggcggtc accctccgca cccgcaagtt 120 catgaccaac cgcctcctgg cccgcaagca attcgtgctt gaggtgatcc accccggccg 180 cgccaacgtc tccaaggcgg agttgaagga gaggcttgcc aaggcgtacg aggtgaagga 240 ccccaacacc atctttgtct tcaagttccg cacccacttc ggaggaggaa agtccactgg 300 tttcggcctc atctacgaca acctcgaggc tgccaagaag ttcgagccga aataccgcct 360 catcaggaat ggtcttgcta ctaaggttga gaagtcccgc aagcaaatga aggagcggaa 420 gaacagggcc aagaagatcc gtggtgtcaa gaagaccaaa gctggtgacg ccaagaagaa 480 gtaaacgttc gtttacattt gtattactgt tctg 514 32 766 DNA Homo sapiens misc_feature Incyte ID No 370661.3.j 32 cgggaatccg ccgtttgcgc tgaggcaatg gcggcagctg cgccggtngc cgcggacgac 60 gatgagcggc ggcggcggcc gggggctgca ctggaggact cccggtccca ggaaggggca 120 aatggtgagg ccgagtcagg tgagctcagc cggcttcggg ctgagctggg caggcgccct 180 ggcagaaatg gaaaccatga aggctgtggc agaggtgagc gagagcacga aggccgaggc 240 tgtggctgcg gtgcacggca gtgccaagag gaggtggcct cgctgcaggc catcctgaaa 300 gactccatca gcagctatga agcccagatc accgccctga agcaggagcg acanagcagc 360 agcaggactg tgaggagaag gagcgggagc tgggccgcct gaagcagctg ctgtcccggg 420 cctaccccct ggactccctg gagaagcaga tggaaaaggt tgggattggg atggcttccc 480 tgctgccctg ggatttggaa gaatgttgag gactgtggat gtcccattcc ctggtcatgg 540 ggtgcggggc acccagcagt gattctagga atagcacaga gttaccaggt gttgttgaga 600 gcttggctct gtgctccgta gggtcctggc ttgcccctta ttagtgggtg accaagttcg 660 cttagctcca aaattaactt aagttatgta gagggaaggg aacttacact taagggtaac 720 aaaaaaaatt cttactgtta ttaaatattg acttctggtg tacatt 766 33 1416 DNA Homo sapiens misc_feature Incyte ID No 427939.17.j 33 attttttcta aatgtgagat caaggaatta ccaccaaaaa aggagagtaa tacaggagaa 60 atattccaga cagtaatgtt ggaaagacat gaaagccacg acatacaaga tttttgcttc 120 agagaaaccc agaaaaatgt acatgactct cagtgtctgt ggaaacatga ttgaagacat 180 tataagcgag tgcgtgtgac ctataaggaa agtctcattg gtagaagaga catgcatggt 240 agaaaggatg atgcacaaaa gcagcctgtt aaaaatcagc ttggattaaa cccgcagtca 300 catctaccag aactgcagct atttcaagct gaagggaaaa tatataaata tgatcacatg 360 gaaaaatctg tcaacagtag ttccttagtt tccccacccc aacgtatttc ttctactgtc 420 aaaacccaca tttctcatac atatgaatgt aattttgtgg attcattatt cacacaaaaa 480 gagaaagcaa atattgggac agaacactac aaatgtaatg agcgtggcaa ggcctttcat 540 caaggcttac attttactat acatcaaata atccatacta aagagacgca atttaaatgt 600 gatatatgtg gcaagatctt caataaaaaa tcaaaccttg caagtcatca aagaattcat 660 actggagaga agccatataa atgtaatgaa tgtggcaagg tcttccataa tatgtcacac 720 cttgcacagc atcgcaggat tcatactgga gagaaaccat ataaatgtaa tgaatgtggc 780 aaggtcttta atcaaatttc acaccttgca caactatcaa aagaattcat accggagaga 840 aaccttataa atgtaatgaa tgtggaaagg tcttccatca aatttcacac cttgcacaac 900 atcggacaat tcatactgga gaaaaacctt acgaatgtaa caaatgtggc aaggtgttca 960 gtcgcaattc ctaccttgta caacatctga tcattcatac tggagagaaa ccttacagat 1020 gtaatgtatg tggaaaggtc ttccatcata tttcacacct tgcacaacat cagagaatcc 1080 acactggaga gaaaccttac aaatgtaatg agtgtggcaa ggtcttcagt cacaagtcat 1140 ccctagtaaa tcactggaga attcatactg gagagaaacc ttacaaatgt aatgagtgtg 1200 gcaaggtctt cagtcacaag tcatccctag taaatcactg gagaatccac actggagaga 1260 aaccttacaa atgtaatgaa tgtngcaagg tcttcagtcg caattcatac cttgcccaac 1320 atctgataat tcatggccgg tgagaaacct tataagtgtg atgaatgtga caaagcattc 1380 agtcaaaatt cacatgcttg tacaacatca cngaat 1416 34 441 DNA Homo sapiens misc_feature Incyte ID No 430569.2.j 34 aacacttgcg ttgtaatcaa ctacgtgaat aagtgttgtt attcttacct acagaagcca 60 ggttcctgaa gatttcttgc atcacatctc tgtagagatt cttttgagaa ggatccagca 120 aagcccactc ctcctgagta aaggccacag ccacatcttc aaatgacact gaatcctaga 180 atatcgcaca tatgtggaga ggaggatggc ttagacagac agtactaaga atctatactc 240 atctcataaa atcgtaacat aattctgcag acttcaaaca tttcttccat gacctggtca 300 tcagaacttt actctctgtc tgcacttact gctgcccact caacattctt catgctaaaa 360 tgaaactatt cagaaagtca acagcagagt aggaacacct gtctcattgg caggtgcagg 420 gaataaactg tgctgaaaga a 441 35 275 DNA Homo sapiens misc_feature Incyte ID No 444689.1.j 35 ctatgcaggt tgttgtcggg ataccagatt tcctactccg agangccccg ggtccctctg 60 ccacaacttc tgtcgctctg ccgcctgcac cgtgacccgc actattcacg ggagccctag 120 agaggacacc gggacaccca gaagccggga aatgatgttt caggattcag tggcctttga 180 ggatgtggct gtcagcttca cccaggagga gtgggctttg ctggatcctt cccagaagaa 240 tctctacagg gatgtgatgc aggaaacctt caaga 275 36 517 DNA Homo sapiens misc_feature Incyte ID No 445198.1.j 36 cttgcagaag gtggttatcc tttacggttc tccacactct ttcaggannc agcagaaaat 60 gaacatatct caggcatcag tgtcattcaa ggacgtgact atagaattca cccaggagga 120 gtggcagcaa atggcccctg ttcagaagaa tctgtacaga gatgtgatgc tggagaacta 180 cagcaacctc gtctcagtgg ggtactgctg tttcaaacca gaggtgatct tcaagttgga 240 gcaaggagag gagccttggt tctcagagga ggaattctca aaccagagtc acccaaaaga 300 ttacagaggt gatgacctga tcaagcagaa caagaaaatc aaagacaaac acttggagca 360 agcaatatgt atcaataata aaacattgac tacagaggaa gagaaagttt tggggaaacc 420 atttactctg catgtagctg ctgttgcttc aacaaaaatg tcctgcaaat gcaactcatg 480 ggaagtgaat ttgcaaagta tttctgaatt tatcatt 517 37 499 DNA Homo sapiens misc_feature Incyte ID No 084399.1 37 ggacatgtcc aggcggaagc aggcgaangc cgctcggtga aagttgaaga gggggaggcc 60 tcagacttct cgctggcctg ggattcctcc gtgacagcag caggaggcct agaaggagag 120 ccagagtgcg atcagnaaac nagccgtgcg ctggaanaca ggaacagcgt gacaagtcaa 180 gaggagagaa atgagggatg atgaagacat ggaggatgaa tcaatttaca cctgcgatca 240 ctgtcagcag gacttcgagt ctctggcaga cctgacggac caccgggccc accgctgtcc 300 tggaggtaat gcaaaacagc cccaggactc tgacaggtgg ttacacgggt aattggacat 360 agcaacagct tgaagcctca agtgagatta aagaattaat aatgtaattt tacagttaat 420 gtcattttat tgtggtgtct tgggtaccct gtatccgcct tttaaataca attaaaaata 480 aaagcaacag ctttccggc 499 38 1017 DNA Homo sapiens misc_feature Incyte ID No 350044.1 38 ctggcggagg ccttgctgat gaacctgact gagggtcccc tggcgatggc agaaatggac 60 cctacacagg gccgtgtggt ctttgaggac gtggccatat atttctccca ggaggagtgg 120 gggcaccttg atgaggctca gagattgctg taccgtgatg tgatgctgga gaatttggcc 180 cttttgtcct cactaggttc ttggcatgga gctgaggatg aggaggcacc ttcacagcaa 240 ggtttttctg taggagtgtc agaggttaca acttcaaagc cctgtctgtc cagccagaag 300 gtccacccta gtgagacatg tggcccaccc ttgaaagaca ttctgtgcct ggttgagcac 360 aatggaattc atcctgagca acacatatat atttgtgagg cagagctttt tcagcaccca 420 aagcagcaaa ttggagaaaa tctttccaga ggggatgatt ggataccttc atttgggaag 480 aaccacagag ttcacatggc agaggagatc ttcacatgca tggagggctg gaaggactta 540 ccagccacct catgccttct ccagcaccag ggccctcaaa gcgagtggaa gccatacagg 600 gacacagagg acagagaagc ctttcagact ggacaaaatg attacaaatg tagtgaatgt 660 gggaaaacct tcacctgcag ctattcattt gttgagcacc agaaaatcca cacaggagaa 720 aggtcttatg aatgtaacaa atgtgggaaa ttctttaagt acagtgccaa tttcntgaaa 780 catcagacag ttcacactag tgaaaggact tatgagtgca gagaatgtgg aaaatccttt 840 atgtacaact accgactcat gagacataag cgagttcaca ctggagaaag accttatgag 900 tgcagcgaat gccagaaggc ctttattaga aagtctcacc tggttcatca ccagaaaatc 960 cacagtgaag agaggcttgt gtgctccatg aatgtgggaa ttctttagct aaaactc 1017 39 1231 DNA Homo sapiens misc_feature Incyte ID No 441329.2 39 ttttgcttga taataactat aattactaca aggactgcct gagatgaaaa agacaggtga 60 aatcgaactt tcacatggac tggtgtctga gctggagagt ctgtttgagt ttgagtaggg 120 gaaagcctga aaccccccac cacctgctcc cgttagtccc tgcattaact aggggcggac 180 tgggacctga tcctccaagc tggaggcttg aaaactcaag ggcaggcgcc tggtccagcg 240 attcggaaac cgagatgcaa agtcctcccg cgctcctaga gaggacccgg aagcgcggcg 300 cggtcccgga agacgaggtg gtgacacgct tccggccttt gtgactcatt gtgtctgtgt 360 cgaggcgtcg ggagggccta agtccgtgtg cggtgccctt cggccggcct gagccccaga 420 gtcagctccc ctttctcgcc cagcgccccc aggccgctcc cggggctcac ggaatagtaa 480 agaaacacat cataaaacct cccaggacat aaaggtgagc acagaccctg tttggatcaa 540 gtcagttcct ggagcctgaa tgatgactgc tgaatcacgg gaagccacgg gtctgtcccc 600 acaggctgca caggagaagg atggtatcgt tatagtgaag gtggaagagg aagatgagga 660 agaccacatg tgggggcagg attccaccct acaggacacg cctcctccag acccagagat 720 attccgccaa cgcttcaggc gcttctgtta ccagaacact tttggggccc cgagaggctc 780 tcagtcggct gaaggaactt tgtcatcagt ggctgcggcc agaaataaac accaaggaac 840 agatcctgga gcttctggtg ctagagcagt ttctttccat cctgcccaag gagctccagg 900 tctggctgca ggaataccgc cccgatagtg gagaggaggc cgtgaccctt ctagaagact 960 tggagcttga tttatcagga caacaggtcc caggtcaagt tcatggacct gagatgctcg 1020 caagggggat ggtgcctctg gatccagttc aggagtcctc gagctttgac cttcatcacg 1080 aggccaccca gtcccacttc aaacattcgt ctcggaaacc ccgcctctta cagtcacgag 1140 gtaagaagca aggtttcatt taggggaagg gaaatgattc aggacgagag tctttgtgct 1200 gctgagtgcc tgtgatgaag aagcatgtta g 1231 40 730 DNA Homo sapiens misc_feature Incyte ID No 442401.2 40 gcggcttccg ggatttggcg gtggcctttg ttggctgcag taagagctca gtctcttcac 60 caggggctcc cagtccttcc atctgggagg ccaaggcggc ttcgcgttct gagaatagac 120 agaacctctg ttactctgtg accggcaggc accgggagat ccgtagctca gacgccagga 180 catcccggaa gctgggaaat ggtgaatgtg ccagggactg ttgacattca gggatgtggc 240 catagaattc tctcgggagg agtgggaaca cctggactca gatcagaagc ttttatatgg 300 ggatgtgatg ttagagaact acggaaacct ggtctctctg ggtctcgctg tctctaagcc 360 ggacctgatc acctttttgg agcaaaggaa agagccctgg aatgtgaaga gtgcagagac 420 agtagccatc cagccagata tcttttctca tgatactcaa ggcctcttaa gaaagaagct 480 tatagaagca tcattccaaa aagtgatatt ggatggatat gggagctgtg gccctcagaa 540 tttaaactta aggaaagagt gggaaagtga gggcaaaata atcctatggt gaaaaaaaat 600 caacaagata atctctgcat gagaaaaagg nccaaagaca agtgaatttt ctgagggtga 660 tgaaagtgtt gcttcgaaaa ggggtgaagt ttatatgggt ctatttattt gtctaacatg 720 tacagttaag 730 41 575 DNA Homo sapiens misc_feature Incyte ID No 444933.2 41 gggtccggcg ctccagaaca gaacgatccc tgaggctccc ttgctcgaac tgtgggactt 60 accctactat ggtccgagcc taccctattt cattatactc aagtaacgcc ccagaaattc 120 cagagaatct cacacaaaga ggttgagtct tgccgtggtg ccttcagggg aatgtcatcc 180 cgggctagaa gagctgcaaa aggctgtcag gcttctcaga actttgcttc tccagcagaa 240 taatcctgcg gaagactgag cagttcttgt gagtgtaaaa ccatggccca tgcattggtg 300 acgttcaggg atgtggctat agacttctct cagaaggaat gggagtgcct ggacactacc 360 cagaggaaat tgtacagaga tgtgatgttg gagaattata ataacttggt ctcactggga 420 tattctggct caaagccaga tgtgattacc ttactggagc aagggaaaga gccctgcgtg 480 gtggcgaggg atgtgacagg aagacagtgc cccggtttgt tatccaggca taagaccaag 540 aaattatctt cagaaaagga cattcatgaa atcag 575 42 734 DNA Homo sapiens misc_feature Incyte ID No 481129.4 42 ggcgtgcgag actcggcggg cgctgttgag ggagtcgggc cgcgactgtg gtcgttttta 60 taccttcccg cgcggacgcc ggcgctgcca acggaagggc gggtagggcg gtgcgtgatt 120 aggttggcga agagacggag tttcgtcatg ttggccaggc ccatttgaga tctttgaaga 180 tatcctcaac gtgaggctct gctgccatga aggtgaagat taagtgctgg aacggcgtgg 240 ccacttggct ctgggtggcc aacgatgaga actgtggcat ctgcaggatg gcatttaacg 300 gatgctgccc tgactgcaag gtgcccggcg acgactgccc gctggtgtgg ggccagtgct 360 cccactgctt ccacatgcat tgcatcctca agtggctgca cgcacagcag gtgcagcagc 420 actgccccat gtgccgccag gaatggaagt tcaaggagtg aggcccgacc tggctctcgc 480 tggaggggca tcctgagact ccttcctcat gctggcgccg atggctgctg gggacagcgc 540 ccctgagctg caacaaggtg gaaacaaggg ctggagctgc gtttgttttg ccatcactat 600 gttgacactt ttatccaata agtgaaaact cattaaacta ctcaaatctt gctggaggcc 660 tctgggtgcc tgtgttctcg gcatatagat gtggtctcgg tgtgttttga tatgaaaact 720 ctaaatgaat aaac 734 43 1104 DNA Homo sapiens misc_feature Incyte ID No 481999.1 43 ctgtcatcca tgctgatatg ctttcatttt gctgtgatag ggagagaatn cacatgtgct 60 tctcggaatt tgtgctgtca ctggagcatt tatttgagtg tctataatgt attcagggtt 120 gtgctaaaac ctgtcagtag agaacaataa gaagaagtca caatctagtt gtgctgagat 180 atattcagtt aggtgaaaga ngtgctcttc aagccatatg actagatgag atcaccggtg 240 aatatgtaca gacaggggag aagaaagtga ggaccatcaa gtgataggag accaaagngt 300 cttgtcaagg catgccaaga caaggtccct cattctccag tcaacatagt ggagaacgta 360 cttgcctgac gccagcatgt gtgtgatggt ttaggactca gtggctttag aggatgtggc 420 tgtgaacttc acccgagaag agtgggcttt gctgggtcct tgtcagaaga atctctacaa 480 agatgtgatg ctggagaact acatgaacct ggcctctgtg gaatgggaaa tacaacctag 540 aaccaaacgg tcatcacttc agcagggttt tttgaagaat caaatattca gtgggataca 600 aatgacaaga ggctacagtg gatggaaact ctgtgactgt aagaattgtg gagaggtctt 660 cagggaacag ttttgcctta agacacacat gagagttcag aatggaggga atacttctga 720 gggtaattgt tatggaaaag acaccctcag tgtgcacaag gaagcctcta ctggacagga 780 actttccaaa tttaatccat gtggaaaagt ctttactcta actccaggtc ttgctgtaca 840 tcttgaagtt ctcaatgcaa gacaacccta caaatgtaag gaatgtggaa aaggctttaa 900 gtatnntgca agccttgata atcatatggg aatccacact gatgagaaac tctgngaatt 960 ncaggnatat gggagagcng tcacagcttc ttcacaccta nagcagtgtg tagcagttca 1020 nacagganag anatccaaaa agactaagaa atgtgggaaa tccttcacta attnttctca 1080 actttatgca cctgtgaaaa ctca 1104 44 665 DNA Homo sapiens misc_feature Incyte ID No 233814.1.j 44 ggagtgtgga agagccatcc agagtgagtg cctggggcag agtgagagca ggaccagcgg 60 gcaggtggcg gacgggggtc ggtggtggat ggcccagccc tggaaagccg aggtgaaggt 120 tacgagtccc tgaggatctg tgggtgtgag ccagccgcgt ggccctgggc aacggcgctg 180 ccggacagaa gtggcggttg ctgacgcctg gaaattcccc tgaaggtgga gcaccaccca 240 acccccctgg gtcccaccct ccctcaaggc ctcctccacc tccacctcca ccccgcctgg 300 cctggcgtcc acctctgcgg ctcctacctg ggtgcaatcg agttaaatgg ctgataagca 360 gatcagcctg ccagccaagc tcatcaatgg cggcatcgcg gggctgatcg gtgtcacctg 420 cgtgtttacc atcgacctgg ccaagacaag gctgcagaac cagcagaacg gccagcgcgt 480 gtacacgagc atgtccgact gcctcatcaa gaccgtccgc tccgagggct acttcggcat 540 gtaccgggga gctgctgtga acttgaccct cgtcaccccc gagaaggcca tcaagctggc 600 agccaacgac ttcttccgac atcagctctc taaggacggg cagaagcttg accctgcttt 660 aaaga 665 45 580 DNA Homo sapiens misc_feature Incyte ID No 351376.4.j 45 agacactgct tgctgcggca gagacgccag aggtgcagct ccagcagcaa tggcagtgac 60 ggcgttggcg gcgcggacgt ggcttggcgt gtggggcgtg aggaccatgc aagcccgagg 120 cttcggctcg gatcagtccg agaatgtcga ccggggcgcg ggctccatcc gggaagccgg 180 tggggccttc ggaaagagag agcaggctga agaggaacga tatttccgac attacaggtt 240 atgctttgag atctctttgg ggtgaaggat tgaaattaaa ccctgagcca ccgtgtcctt 300 gtagagcaca gagtagagaa caactggcag ctttgaaaaa acaccatgaa gaagaaatcg 360 ttcatcataa gaaggagatt gagcgtctgc agaaagaaat tgagcgccat aagcagaaga 420 tcaaaatgct aaaacatgat gattaagtgc acaccgtgtg ccatagaatg gcacatgtca 480 ttgcccactt ctgtgtagac atggttctgg tttaactaat atttgtctgt gtgctactaa 540 cagattataa taaattgtca tcagtgaact gtgaaaaaaa 580 46 1935 DNA Homo sapiens misc_feature Incyte ID No 338992.1 46 tgaaagtact tttactccca agggtatctg atctgatgga gagaatgtat cnctngtacc 60 gatgcggata gaacgctcat tanttacngc acagtnttca taaattccaa cttccctagg 120 aattttgtct tttgaaggca tgttggaagt tggggcatta ggatataatc tcagtccatg 180 tactaagcct ctgcataact gaaagatnga gtcaataaaa ttcactctct cattttttgt 240 ttttaatctc aagaattttt gccttgaagg aaaaatgtag tggagaattt gatgtttgaa 300 cgaatcccag tcagaagttc cagcctgcca ctgttctctg atgccatgcc agcaccaact 360 caactgtttt ttcctctcat ccgtaactgt gaactgagca ggatctatgg cactgcatgt 420 tactgccacc acaaacatct ctgttgttcc tcatcgtaca ttcctcagag tcgactgaga 480 tacacacctc atccagcata tgctaccttt ngtcaggcca aaggagaact ggtggcagta 540 cacccaagga aggagatatg cttccacacc acatacagtc cccctcacac ctccgcaagt 600 caatagcatc cttaaagcta atgaatacag tttcaaagtg ccagactttg acggcaaaaa 660 tgtcagttct atcctgtcga tttgacagca atcagctgcc tgcaaatgca cccattgagg 720 accggagaag tgcagcaacc tgcttgcaga ccagagggct ccttttgggg gtttttgatg 780 gccatgcagg ttgtgcttgt tcccaggcag tcagtgaaag actcttttat tatattgctg 840 tctctttgtt accccatgag actttgctag agattgaaaa tgcagtggag agcggccggg 900 cactgctacc cattctccag tggcacaagc accccaatga ttactttagt aaggaggcat 960 ccaaattgta ctttaacagc ttgaggactt actggcaaga gcttatagac ctcaacactg 1020 gtgagtcgac tgatattgat gttaaggagg ctctaattaa tgccttcaag aggcttgata 1080 atgacatctc cttggaggcg caagttggtg atcctaattc ttttctcaac tacctggtgc 1140 ttcgagtggc attttctgga gccactgctt gtgtggccca tgtggatggt gttgaccttc 1200 atgtgggcca atactggcga tagcagagcc atgctgggtg tgcaggaaga ggacggctca 1260 tggtcagcag tcacgctgtc taatgaccac aatgctcaaa atgaaagaga actagaacgg 1320 ctgaaattgg aacatccaaa gagtgaggcc aagagtgtcg tgaaacagga tcggctgctt 1380 ggcttgctga tgccatttag ggcatttgga gatgtaaagt tcaaatggag cattgacctt 1440 caaaagagag tgatagaatc tggcccagac cagttgaatg acaatgaata taccaagttt 1500 attcctccta attatcacac acctccttat ctcactgctg agccagaggt aacttaccac 1560 cgattaaggc cacaggataa gtttctggtg ttggctactg atgggttgtg ggagactatg 1620 cataggcagg atgtggttag gattgtgggt gagtacctaa ctggcatgca tcaccaacag 1680 ccaatagctg ttggtggcta caaggtgact ctgggacaga tgcatggcct tttaacagaa 1740 aggagaacca aaatgtcctc ggtatttgag gatcagaacg cagcaaccca tctcattcgc 1800 cacgctgtgg gcaacaacga gtttgggact gttgatcatg agcgcctctc taaaatgctt 1860 agtcttcctg aagagcttgc tcgaatgtac agagatgaca ttacaatcat tgtcgttcag 1920 ttcaattctc atgtt 1935 47 1709 DNA Homo sapiens misc_feature Incyte ID No 200587.3.j 47 gcccggcagc agtggggcgg ggatggaggc ggccgtggcg ccggggaggg atgcgccggc 60 acccgcggcg agtcagccca gcggctgcgg gaaacacaac tcgccggaga ggaaagttta 120 tatggactat aatgcaacga ctcccctgga gccagaagtt atccaggcca tgaccaaggc 180 catgtgggaa gcctggggaa atcccagcag cccgtattca gcaggaagaa aggccaagga 240 tattataaat gcagctcggg aaagcctcgc gaagatgata ggggggaaac ctcaagatat 300 aatcttcact tccgggggca ctgagtcaaa taatttagta atccattctg tggtgaaaca 360 tttccacgca aaccagacct caaagggaca cacaggtggg caccacagcc cagtgaaggg 420 ggccaagccc catttcatta cttcctcggt ggaacacgac tccatccggc tgcccctgga 480 gcacctggtg gaagaacaag tggcagcggt cacctttgtc ccggtgtcca aggtgagcgg 540 gcaggcagag gtggacgaca tcctcgcggc agtccgcccg accacacgcc tcgtgaccat 600 catgctggcc aacaatgaga ctggcattgt catgcctgtc cctgaaatca gtcagcgcat 660 taaagccctg aaccaggaac gggtggcagc tgggctacct cccatcctcg tgcacacgga 720 tgctgcacag gccttgggga agcagcgcgt ggatgtggag gacctgggcg tggacttcct 780 tacaatcgtg gggcacaagt tttatggtcc caggattggc gcactttata tacgaggact 840 tggtgaattt acccctctct accctatgct atttggaggt ggacaagaac ggaatttcag 900 gccagggaca gagaacaccc caatgattgc tggccttggg aaggtgagcc ctggtgagct 960 tgaggagatg agttgattgc cttgtcatca gtgtccccag cggctctagt aggaatctgg 1020 ggctttaggg agatcatatt cgtgatctca taagcggact gacaagaaaa agcctggaat 1080 ctgatttatc aacctggaga gctgtacttt ttcagatctg tggattagtg gcacttgttt 1140 agcatttaaa agggaaaaac tccttgtctg tgtctcttct gacatgagaa acagtgatac 1200 tgttacagca gaggtgaagt gtcaagctgt aggttcacca ttcccaaagg cgtcggcagc 1260 ccccgcacca tcgacgttct gtccccgatt ggtctgtggg gtggccaatc cagcacctgc 1320 caccagccct ccactggggc ctgtcctgct tctgcgacag taaccaggct caggttttgc 1380 cgtgcgaagg cagaggtact ggttacacct cggcgtctgc aggctgctcc ctcactgtgc 1440 ggcctctggt caaaggccac caccttcaag caaccctcca tgaaccacag ctacattggt 1500 tcccccatgt cccctgctgt caccctctat ccctgacact gctttatttc ccctatctga 1560 tgtttctctg tagtgtgttc agatgtatgc cccaccttct gcttccccga gagcaggggc 1620 ttggccatgt cggcctcagt atccccagta cagagaaagg gcttagcgcc caggaggccg 1680 ggccttggga agagtatgaa tggattccc 1709 48 766 DNA Homo sapiens misc_feature Incyte ID No 246727.5.j 48 ggccgaggtg cgggtcgcct ccagaggtgc gtggtcgtgg cgcgagggat cctgaggctg 60 ctccagcagt gcgccgccgc cgtctcctgg ggcggcttgg gttagccggg aggtgggtca 120 gaggctcgcc ccgtgccctg cgtccgggcg tctccttagg gcgcgtcttc gggtccggcc 180 agcggtgctg aaaaagggag aaggttgggg gtagggagga aacaagatcc cagttcaata 240 gatttctccg cagatcctgt gccttcaaac cctacgagtc catactttaa aacaaaatga 300 agaaagtaag gcttaaggaa ctagagagtc gcctgcaaca agtggatgga tttgaaaagc 360 ccaagctact tctggaacag tatcctacca ggccgcacat tgcagcatgt atgctctata 420 caatccataa cacttatgat gacattgaaa ataaagtcgt tgcagatcta ggatgtggtt 480 gtggagtact tagcatcgga actgcaatgt taggagcagg ggacagatat ggcttttcta 540 aagactgctt tggaaatggc aagaacagca gtatattcct tacacaaatc ctcaactaga 600 gaacatgttc aaaagaaagc tgcagaatgg aaaatcaaga tagatattat agcagaactt 660 cgatatgacc tgccagcatc atacaagttt cacaaaaaga aatcagtgga cattgaagtg 720 gacctaattc ggttttcctt ttaaaagccc cgcaaacaaa agtcgt 766 49 2757 DNA Homo sapiens misc_feature Incyte ID No 407087.3.j 49 gcgggagcaa gtgcggctgg agctgagctt cgtcaactca gacctgcaga tgctcaagga 60 agagctggag gggctgaaca tctcggtggg cgtctatcag aacacagagg aggcatttac 120 gattcccctg attcctcttg gcctgaagga aacgaaagac gtcgactttg cagtcgtcct 180 caaggatttt atcctggaac attacagtga agatggctat ttatatgaag atgaaattgc 240 agatcttatg gatctgagac aagcttgtcg gacgcctagc cgggatgagg ccggggtgga 300 actgctgatg acatacttca tccagctggg ctttgtcgag agtcgattct tcccgcccac 360 acggcagatg ggactcctgt tcacctggta tgactctctc accggggttc cggtcagcca 420 gcagaacctg ctgctggaga aggccagtgt cctgttcaac actggggccc tctacaccca 480 gattgggacc cggtgtgatc ggcagacgca ggctgggctg gagagtgcca tagatgcctt 540 tcagagagcc gcaggggttt taaattacct gaaagacaca tttacccata ctccaagtta 600 cgacatgagc cctgccatgc tcagcgtgct cgtcaaaatg atgcttgcac aagcccaaga 660 aagcgtgttt gagaaaatca gccttcctgg gatccggaat gaattcttca tgctggtgaa 720 ggtggctcag gaggctgcta aggtgggaga ggtctaccaa cagctacacg cagccatgag 780 ccaggcgccg gtgaaagata acatccccta ctcctgggcc agcttagcct gcgtgaaggc 840 ccaccactac gcggccctgg cccactactt cactgccatc ctcctcatng accaccaggt 900 gaagccaggc acggatntgg accaccagga gaagtgcctg tcccagctct acgaccacat 960 gccagagggg ctgacaccct tggccacact gaagaatgat cagcagcgcc gacagctggg 1020 gaagtcccac ttgcgcagag ccatggctca tcangaggag tcggtgcggg aggcgagcct 1080 ctgcaagaag ctccgganat tgaggtgcta cagaaggtgt gngtgccgca caggaacgct 1140 cccggctcac gtacgcccag caccaggagg aggatgacct gctgaacctg atcgacgccc 1200 ccagtgttgt tgctaaaact gagcaagagg ttgacattat attgccccat tctccaagct 1260 gacagtcacg gacttcttcc agaagctggg ccccttatct gtgttttcgg ctaacaagcg 1320 gtggacgcct cctcgaagca tccgcttcac tgcagaagaa ggggacttgg ggttcacctt 1380 gagagggaac gcccccgttc aggttcactt cctggatcct tactgctctg cctcggtggc 1440 aggagcccgg gaaggagatt atattgtctc cattcagctt gtggattgta agtggctgac 1500 gctgagtgag gttatgaagc tgctgaagag ctttggcgag gacgagattc gagatgaaag 1560 tcgtgagcct cctggactcc acatcatcca tgcataataa gagtgccaca tactccgtgg 1620 gaatgcagaa aacgtactcc atgatctgct tagccattga tgatgacgac aaaactgata 1680 aaaccaagaa aatctccaag aagctttcct tcctgagttg gggcaccaac aagaacagac 1740 agaagtcagc ccagcacctt gtgcctccca tcggtcgggg ctgcacggcc tcaggtcaag 1800 aagaagctgc cctccccttt cagccttctc aactcagaca gttcttggta ctaatgtgag 1860 gaaacaaaca tgttcaggcc ctgaacattt ccggtgctga ctcggcctta aacgtttgtg 1920 ccataatgga aaatatctat ctatctgttc tcaaatcctg tttttctcat agtgtaaact 1980 cacatttgat gtgtttttat gaaggaaagt aaccaagaaa cctctaggaa ttagtgaaaa 2040 aagaactttt ttgaggtgtg ttactatact gctgtaagtt atttattata taaagtattg 2100 taaatagaat agtgttgaag atatgaaata tggctatttt taatggtgac aattatgact 2160 tttagtcact attaaattgg ggttacctat atcagtacaa tttgtagttg tttccaggtt 2220 tggctaataa tcattcctta acctagaatt cagatgatcc tggaattaag gcaggtcaga 2280 ggactgtaat gatagaatta aattagtgtc actaaaaact gtcccaaagt gctgcttcct 2340 aataggaatt cattaaccta aaacaagatg ttactattat atcgatagac tatgaatgct 2400 atttctagaa aaagtctagt gccaaatttg tcttattaaa taaaaacaat gtaggagcag 2460 cttttcttct agtttgatgt catttaagaa ttactaacac agtggcagtg ttagatgaag 2520 atgctgtcta caaggtagat aatatactgt ttgatactca aaacattttt cattttgttt 2580 aaagtagaag ttacataatt ctatatttta agtcttgggt aaaaaagtag ttttacattt 2640 tataaagtaa agatgtaaat gattcaggtt taaagctcta tttgacttcc tttttttgtt 2700 tgagatagcg tcttgctgtg ttgcccaggc tgggagtgca gtgggtgtga tctcgag 2757 50 558 DNA Homo sapiens misc_feature Incyte ID No 441779.1.j 50 atggaggagc tatggacgtc gcaatgcacg cgtacgtaaa gctcggaatt cggctcgagg 60 actcaggaag caatcatggt gctctctgca gctgacaaaa ccaacatcaa gaactgctgg 120 gggaagattg gtggccatgg tggtgaatat ggcgaggagg ccctacagag gatgttcgct 180 gccttcccca ccaccaagac ctacttctct cacattgatg taagccccgg ctctgcccag 240 gtcaaggctc acggcaagaa ggttgctgat gccctggcca aagctgcaga ccacgtcgaa 300 gacctgcctg gtgccctgtc cactctgagc gacctgcatg cccacaaact gcgtgtggat 360 cctgtcaact tcaagttcct gagccactgc ctgctggtga ccttggcttg ccaccaccct 420 ggggatttca cacctgccat gcacgcctct ctggacaaat tccttgcctc tgtgagcacc 480 gtgctgacct ccaagtaccg ttaagccacc tcctgtcggg cttgccttct gaccaggccc 540 ttcttccgtc ccctgaac 558 51 905 DNA Homo sapiens misc_feature Incyte ID No 206603.1 51 gggccgcggc cggcagaagg gctgttagga gggaccacgc gccgggggcc gcgatctctg 60 gcagggggcg gtgtgccagc ggagcaccat gcacataggc gcccagcgcc ccgactaccc 120 ctcccgagga aaagaggccg gggccgcgct ggggcggcgg agagcatgag ggaggccggg 180 gggcggctcg gcttggagcg ctgctaggga gcggtgcgcg ccgcacaccc gcctgggcgc 240 ggcggagggc ggggagccgg gcaggtcgcg cctgcgggcg gcagccgacc gccgggagct 300 gttctgattt ccgacgcgca cgctaggggc ccggagcagc ccccggcccc ggcgcgccgc 360 cgacatgggc aacngcaggg agcattggat tcgcagcaga ccgatttcag ggcgcacaac 420 cgtgcctttg aagctgccga tgccagagcc aggtgaactg gaggagcgat ttgccatcgt 480 gctgaatgct atgaacctac ctcctgacaa agccaggtta ctgcggcagt atgataatga 540 gaaaaaatgg gaactgattt gtgatcagga acgattccag gtgaagaatc ctccccatac 600 atacattcaa aagctcaaag gctatctgga tccagctgta accaggaaga aattcagacg 660 gcgtgttcaa gaatctacac aagtgctaag agaactggaa atttctttga gaactaacca 720 cattggatgg gtcagagaat ttctgaatga agaaaacaaa ggtcttgatg ttctagtgga 780 atatctctca tttgcacagt acgcgagaac ttttgacttt gaaagtgtgg agagtactgt 840 ggagagctcg gtggacaaat caaagccctg gagtaggtcc atcgaggacc tgcacagagg 900 gagca 905 52 2160 DNA Homo sapiens misc_feature Incyte ID No 435694.2 52 cgttcttttc ctttctcctt gaaagagtga atgcatttgg tcgcagggct aaagaggagg 60 atgctatact tttctaaatg gcaagagatg gggagagaag gggattaaga gttgacccgc 120 aacctcccgg ggattctttg ttcttaccag atctcttggc cactccccta ttctgaagtc 180 gtcttggctc tcttgactgc tcccctattc tgaagtcgtc ttggctctct tgactgctcc 240 cctattctga agtcgtcttg gctctcctga ctacactatt tcaaggaatg atcaccaaga 300 cacacaaagt agaccttggg ctcccagaga agaaaaagaa gaagaaagtg gtcaaagaac 360 cagagactcg atactcagtt ttaaacaatg atgattactt tgctgatgtt tctcctttaa 420 gagctacatc cccctctaag agtgtggccc atgggcaggc acctgagatg cctctagtga 480 aganaaanaa naanaaaaag aagggtgtca gcaccctttg cgaggagcat gtagaacctg 540 agaccacgct gcctgctaga cggacagaga agtcacccag cctcaggaag caggtgtttg 600 gccacttgga gttcctcagt ggggaaaaga aaaataagaa gtcacctcta gccatgtccc 660 atgcctctgg ggtgaaaacc tccccagacc ctagacaggg tgaggaggaa accagagttg 720 gcaagaagct caaaaaacac aagaaggaaa aaaagggggc ccaggacccc acagccttct 780 cggtccagga cccttggttc tgtgaggcca gggaggccag ggatgttggg gacacttgct 840 cagtggggaa gaaggatgag gaacaggcag ccttggggca gaaacggaag cggaagagcc 900 ccagagaaca caatgggaag gtgaagaaga aaaaaaaaat ccaccaggag ggagatgccc 960 tcccaggcca ctccaagccc tccaggtcca tggagagcag ccctaggaaa ggaagtaaaa 1020 agaagccagt caaagttgag gctccggaat acatccccat aagtgatgac cctaaggcct 1080 ccgcaaagaa aaagatgaag tccaaaaaga aggtagagca gccagtcatc gaggagccag 1140 ctctgaaaag gaagaaaaag aagaagagga aagagagtgg ggtagcagga gacccttgga 1200 aggaggaaac agacacggac ttagaggtgg tgttggaaaa aaaaggcaac atggatgagg 1260 cgcacataga ccaggtgagg cgaaaggcct tgcaagaaga gatcgatcgc gagtcaggca 1320 aaacggaagc ttctgaaacc aggaagtgga cgggaaccca gtttggccag tgggatactg 1380 ctggttttga gaacgaggac caaaaactga aatttctcag acttatgggt ggcttcaaaa 1440 acctgtcccc ttcgttcagc cgccccgcca gcacgattgc aaggcccaac atggccctcg 1500 gcaagaaggc ggctgacagc ctgcagcaga atctgcagcg ggactacgac cgggccatga 1560 gctggaagta cagccgggga gccggcctcg gcttctccac cgcccccaac aagatctttt 1620 acattgacag gaacgcttcc aagtcagtca agctggaaga ttaaactcta gagttttgtc 1680 cccccaaaac tgccacaatt gctttgatta ttccatttat gctggagatt acaaattttt 1740 tttgtgaaaa aatcagatct tggtgaggac ctcgagcagt aagatataaa taactcccat 1800 aagcttagcg ttccagtaat ggaacactag gcataaatgg tttattcagt tgtgcaaatg 1860 aaagccatct gacagttggc tcacattgaa cacctgtgga gattaaggac gaggacaact 1920 atattgatgg gcttggatga actggggcag ggcagctcat atttcgggag ccaggagaac 1980 gagtgagtgc taaaacctcc tgttttctgt gttaaacatt ccgtccctgt ttgagacatc 2040 agtatgtaca gttaactttt gttgagtgtt tagcaggtac tagggacata ctagtgtttt 2100 ccttaatgta tttaatcttc ataattatga aatgggtgct attattagcc ccatcttata 2160 53 190 PRT Homo sapiens misc_feature Incyte ID No 061149.1.j.orf1 53 Glu Lys Ser Asn Lys Leu Leu Leu Ala Leu Val Met Leu Phe Leu 1 5 10 15 Phe Ala Val Ile Val Leu Gln Tyr Val Cys Pro Gly Thr Glu Cys 20 25 30 Gln Xaa Leu Arg Leu Gln Ala Phe Ser Ser Pro Val Pro Asp Pro 35 40 45 Tyr Arg Ser Glu Asp Glu Ser Ser Ala Arg Phe Val Pro Arg Tyr 50 55 60 Asn Phe Thr Arg Gly Asp Leu Leu Arg Lys Val Asp Phe Asp Ile 65 70 75 Lys Gly Asp Asp Leu Ile Val Phe Leu His Ile Gln Lys Thr Gly 80 85 90 Gly Thr Thr Phe Gly Arg His Leu Val Arg Asn Ile Gln Leu Glu 95 100 105 Gln Pro Cys Glu Cys Arg Val Gly Gln Lys Lys Cys Thr Cys His 110 115 120 Arg Pro Gly Lys Arg Glu Thr Trp Leu Phe Ser Arg Phe Ser Thr 125 130 135 Gly Trp Ser Cys Gly Leu His Ala Asp Trp Thr Glu Leu Thr Ser 140 145 150 Cys Val Pro Ser Val Val Asp Gly Lys Arg Asp Ala Arg Leu Arg 155 160 165 Pro Ser Ser Leu Gln Gln Asn His Leu Ala Arg Arg Cys Leu Leu 170 175 180 Lys Lys Ile Arg Ser Phe Ile Gln Lys Arg 185 190 54 120 PRT Homo sapiens misc_feature Incyte ID No 404508.3.j.orf3 54 Glu Arg Met Thr Ala Arg Glu Glu Ala Ser Leu Arg Thr Leu Glu 1 5 10 15 Gly Arg Arg Arg Ala Thr Leu Leu Ser Ala Arg Gln Gly Met Met 20 25 30 Ser Ala Arg Gly Asp Phe Leu Asn Tyr Ala Leu Ser Leu Met Arg 35 40 45 Ser His Asn Asp Glu His Ser Asp Val Leu Pro Val Leu Asp Val 50 55 60 Cys Ser Leu Lys His Val Ala Xaa Val Phe Gln Ala Leu Ile Tyr 65 70 75 Trp Ile Lys Ala Met Asn Gln Gln Thr Thr Leu Asp Thr Pro Gln 80 85 90 Leu Glu Arg Lys Arg Thr Arg Glu Leu Leu Glu Leu Gly Ile Asp 95 100 105 Asn Glu Asp Ser Glu His Glu Asn Asp Asp Asp Thr Asn Gln Ser 110 115 120 55 272 PRT Homo sapiens misc_feature Incyte ID No 441227.2.j.orf3 55 Ala Ala Trp Asp Arg Gly Lys Arg Ser Leu Val Leu Asp Leu Lys 1 5 10 15 Gln Pro Arg Gly Ala Ala Val Leu Arg Arg Leu Cys Lys Arg Ser 20 25 30 Asp Val Leu Leu Glu Pro Phe Arg Arg Gly Val Met Glu Lys Leu 35 40 45 Gln Leu Gly Pro Glu Ile Leu Gln Arg Glu Asn Pro Arg Leu Ile 50 55 60 Tyr Ala Arg Leu Ser Gly Phe Gly Gln Ser Gly Ser Phe Cys Arg 65 70 75 Leu Ala Gly His Asp Ile Asn Tyr Leu Ala Leu Ser Gly Val Leu 80 85 90 Ser Lys Ile Gly Arg Ser Gly Glu Asn Pro Tyr Ala Pro Leu Asn 95 100 105 Leu Leu Ala Asp Phe Ala Gly Gly Gly Leu Met Cys Ala Leu Gly 110 115 120 Ile Ile Met Ala Leu Phe Asp Arg Thr Arg Thr Asp Lys Gly Gln 125 130 135 Val Ile Asp Ala Asn Met Val Glu Gly Thr Ala Tyr Leu Ser Ser 140 145 150 Phe Leu Trp Lys Thr Gln Lys Ser Ser Leu Trp Glu Ala Pro Arg 155 160 165 Gly Gln Asn Met Leu Asp Gly Gly Ala Pro Phe Tyr Thr Thr Tyr 170 175 180 Arg Thr Ala Asp Gly Glu Phe Met Ala Val Gly Ala Ile Glu Pro 185 190 195 Gln Phe Tyr Glu Leu Leu Ile Lys Gly Leu Gly Leu Lys Ser Asp 200 205 210 Glu Leu Pro Asn Gln Met Ser Met Asp Asp Trp Pro Glu Met Lys 215 220 225 Lys Lys Phe Ala Asp Val Phe Ala Lys Lys Thr Lys Ala Glu Trp 230 235 240 Cys Gln Ile Phe Asp Gly Thr Asp Ala Cys Val Thr Pro Val Leu 245 250 255 Thr Phe Glu Glu Val Val His His Asp His Asn Lys Glu Arg Gly 260 265 270 Ser Phe 56 212 PRT Homo sapiens misc_feature Incyte ID No 277927.2.orf3 56 Thr Pro Asn Pro Leu Glu Ala His Arg Asp Arg Asp Ser Lys Arg 1 5 10 15 Ser Arg Asp Lys Tyr Thr His Ala Arg Ser Ser Leu Ala Leu Ser 20 25 30 Leu Ser Leu Ser Leu Leu Pro Pro Ser Leu Ser Ala Cys Pro Ser 35 40 45 Pro Leu Val Leu Lys Phe Pro Val Pro Cys Thr Pro Ser Trp Asp 50 55 60 Thr Met Leu Phe Ser Ala Leu Leu Leu Glu Val Ile Trp Ile Leu 65 70 75 Ala Ala Asp Gly Gly Gln His Trp Thr Tyr Glu Gly Pro His Gly 80 85 90 Gln Asp His Trp Pro Ala Ser Tyr Pro Glu Cys Gly Asn Asn Ala 95 100 105 Gln Ser Pro Ile Asp Ile Gln Thr Asp Ser Val Thr Phe Asp Pro 110 115 120 Asp Leu Pro Ala Leu Gln Pro His Gly Tyr Asp Gln Pro Gly Thr 125 130 135 Glu Pro Leu Asp Leu His Asn Asn Gly His Thr Val Gln Leu Ser 140 145 150 Leu Pro Ser Thr Leu Tyr Leu Gly Gly Leu Pro Arg Lys Tyr Val 155 160 165 Ala Ala Gln Leu His Leu His Trp Gly Gln Lys Gly Ser Pro Cys 170 175 180 Gly Ser Glu His Gln Ile Asn Ser Glu Ala Thr Phe Ala Glu Leu 185 190 195 His Ile Val His Tyr Asp Ser Asp Ser Tyr Asp Ser Leu Ser Glu 200 205 210 Ala Cys 57 154 PRT Homo sapiens misc_feature Incyte ID No 475311.1.orf3 57 Ala Ser Ile Leu Gly Trp Arg Arg Trp Arg Pro Leu Arg Leu Gly 1 5 10 15 Val Lys Thr Ala Gly Met Val Gly Arg Glu Lys Glu Leu Ser Ile 20 25 30 His Phe Val Pro Gly Ser Cys Arg Leu Val Glu Glu Glu Val Asn 35 40 45 Ile Pro Asn Arg Arg Val Leu Val Thr Gly Ala Thr Gly Leu Leu 50 55 60 Gly Arg Ala Val His Lys Glu Phe Gln Gln Asn Asn Trp His Ala 65 70 75 Val Gly Cys Gly Phe Arg Arg Ala Arg Pro Lys Phe Glu Gln Val 80 85 90 Asn Leu Leu Asp Ser Asn Ala Val His His Ile Ile His Asp Phe 95 100 105 Gln Pro His Val Ile Val His Cys Ala Ala Glu Arg Arg Pro Asp 110 115 120 Val Val Glu Asn Gln Pro Asp Ala Ala Ser Gln Leu Asn Val Asp 125 130 135 Ala Ser Gly Asn Leu Ala Lys Glu Ala Ala Ala Val Gly Ala Phe 140 145 150 Pro His Leu His 58 525 PRT Homo sapiens misc_feature Incyte ID No 013039.2.orf1 58 Pro Lys Ala Lys Glu Ile Gln Leu Arg Trp Gly Pro Pro Leu Val 1 5 10 15 Asp Gly Gly Ser Pro Ile Ser Cys Tyr Ser Val Glu Met Ser Pro 20 25 30 Ile Glu Lys Asp Glu Pro Arg Glu Val Tyr Gln Gly Ser Glu Val 35 40 45 Glu Cys Thr Val Ser Ser Leu Leu Pro Gly Lys Thr Tyr Ser Phe 50 55 60 Arg Leu Arg Ala Ala Asn Lys Met Gly Phe Gly Pro Phe Ser Glu 65 70 75 Lys Cys Asp Ile Thr Thr Ala Pro Gly Pro Pro Asp Gln Cys Lys 80 85 90 Pro Pro Gln Val Thr Cys Arg Ser Ala Thr Cys Ala Gln Val Asn 95 100 105 Trp Glu Val Pro Leu Ser Asn Gly Thr Asp Val Thr Glu Tyr Arg 110 115 120 Leu Glu Trp Gly Gly Val Glu Gly Ser Met Gln Ile Cys Tyr Cys 125 130 135 Gly Pro Gly Leu Ser Tyr Glu Ile Lys Gly Leu Ser Pro Ala Thr 140 145 150 Thr Tyr Tyr Cys Arg Val Gln Ala Leu Ser Val Val Gly Ala Gly 155 160 165 Pro Phe Ser Glu Val Val Ala Cys Val Thr Pro Pro Ser Val Pro 170 175 180 Gly Ile Val Thr Cys Leu Gln Glu Ile Ser Asp Asp Glu Ile Glu 185 190 195 Asn Pro His Tyr Ser Pro Ser Thr Cys Leu Ala Ile Ser Trp Glu 200 205 210 Lys Pro Cys Asp His Gly Ser Glu Ile Leu Ala Tyr Ser Ile Asp 215 220 225 Phe Gly Asp Lys Gln Ser Leu Thr Val Gly Lys Val Thr Ser Tyr 230 235 240 Ile Ile Asn Asn Leu Gln Pro Asp Thr Thr Tyr Arg Ile Arg Ile 245 250 255 Gln Ala Leu Asn Ser Leu Gly Ala Gly Pro Phe Ser His Met Ile 260 265 270 Lys Leu Lys Thr Lys Pro Leu Pro Pro Asp Pro Pro Arg Leu Glu 275 280 285 Cys Val Ala Phe Ser His Gln Asn Leu Lys Leu Lys Trp Gly Glu 290 295 300 Gly Thr Pro Lys Thr Leu Ser Thr Asp Ser Ile Gln Tyr His Leu 305 310 315 Gln Met Glu Asp Lys Asn Gly Arg Phe Val Ser Leu Tyr Arg Gly 320 325 330 Pro Cys His Thr Tyr Lys Val Gln Arg Leu Asn Glu Ser Thr Ser 335 340 345 Tyr Lys Phe Cys Ile Gln Ala Cys Asn Glu Ala Gly Glu Gly Pro 350 355 360 Leu Ser Gln Glu Tyr Ile Phe Thr Thr Pro Lys Ser Val Pro Ala 365 370 375 Ala Leu Lys Ala Pro Lys Ile Glu Lys Val Asn Asp His Ile Cys 380 385 390 Glu Ile Thr Trp Glu Cys Leu Gln Pro Met Lys Gly Asp Pro Val 395 400 405 Ile Tyr Ser Leu Gln Val Met Leu Gly Lys Asp Ser Glu Phe Lys 410 415 420 Gln Ile Tyr Lys Gly Pro Asp Ser Ser Phe Arg Tyr Ser Ser Leu 425 430 435 Gln Leu Asn Cys Glu Tyr Arg Phe Arg Val Cys Ala Ile Arg Gln 440 445 450 Cys Gln Asp Ser Leu Gly His Gln Asp Leu Val Gly Pro Tyr Ser 455 460 465 Thr Thr Val Leu Phe Ile Ser Gln Arg Thr Glu Pro Pro Ala Ser 470 475 480 Thr Asn Arg Asp Thr Val Glu Ser Thr Arg Thr Arg Arg Ala Leu 485 490 495 Ser Asp Glu Gln Cys Ala Ala Val Ile Leu Val Leu Phe Ala Phe 500 505 510 Phe Ser Ile Leu Ile Ala Phe Ile Ile Gln Tyr Phe Val Ile Lys 515 520 525 59 241 PRT Homo sapiens misc_feature Incyte ID No 238005.4.orf3 59 Ser Ser Trp Gly Leu Ala Phe Gly His Leu Glu Ser Lys Ser Ser 1 5 10 15 Ile Lys Arg Val Leu Ala Ile Thr Thr Val Leu Ser Leu Ala Tyr 20 25 30 Ser Val Thr Gln Gly Thr Leu Glu Ile Leu Tyr Pro Asp Ala His 35 40 45 Leu Ser Ala Glu Asp Phe Asn Ile Tyr Gly His Gly Gly Arg Gln 50 55 60 Phe Trp Leu Val Ser Ser Cys Phe Phe Phe Leu Val Tyr Ser Leu 65 70 75 Val Val Ile Leu Pro Lys Thr Pro Leu Lys Glu Arg Ile Ser Leu 80 85 90 Pro Ser Arg Arg Ser Phe Tyr Val Tyr Ala Gly Ile Leu Ala Leu 95 100 105 Leu Asn Leu Leu Gln Gly Leu Gly Ser Val Leu Leu Cys Phe Asp 110 115 120 Ile Ile Glu Gly Leu Cys Cys Val Asp Ala Thr Thr Phe Leu Tyr 125 130 135 Phe Ser Phe Phe Ala Pro Leu Ile Tyr Val Ala Phe Leu Arg Gly 140 145 150 Phe Phe Gly Ser Glu Pro Lys Ile Leu Phe Ser Tyr Lys Cys Gln 155 160 165 Val Asp Glu Thr Glu Glu Pro Asp Val His Leu Pro Gln Pro Tyr 170 175 180 Ala Val Ala Arg Arg Glu Gly Leu Glu Ala Ala Gly Ala Ala Gly 185 190 195 Ala Ser Ala Ala Ser Tyr Ser Ser Thr Gln Phe Asp Ser Ala Gly 200 205 210 Gly Val Ala Tyr Leu Asp Asp Ile Ala Ser Met Pro Cys His Thr 215 220 225 Gly Ser Ile Asn Ser Thr Asp Ser Glu Arg Trp Lys Ala Ile Asn 230 235 240 Ala 60 115 PRT Homo sapiens misc_feature Incyte ID No 345322.1.j.orf3 60 Leu Ile Ile Ile Ile Thr Met Glu Pro Asn Ser Pro Lys Lys Ile 1 5 10 15 Gln Phe Ala Val Pro Val Phe Gln Ser Gln Ile Ala Pro Glu Ala 20 25 30 Ala Glu Gln Ile Arg Lys Arg Arg Pro Thr Pro Ala Ser Leu Val 35 40 45 Ile Leu Asn Glu His Asn Pro Pro Glu Ile Asp Asp Lys Arg Gly 50 55 60 Pro Asn Thr Gln Gly Glu Leu Gln Asn Ala Ser Pro Lys Gln Arg 65 70 75 Lys Gln Ser Val Tyr Thr Pro Pro Thr Ile Lys Gly Val Lys His 80 85 90 Leu Lys Gly Gln Asn Glu Ser Ala Phe Pro Glu Glu Glu Glu Gly 95 100 105 Thr Asn Glu Arg Glu Glu Gln Arg Asp His 110 115 61 226 PRT Homo sapiens misc_feature Incyte ID No 348094.6.j.orf3 61 Val Leu Lys Phe Leu Leu Leu Gln Thr Met Asp Glu Gln Ser Gln 1 5 10 15 Gly Met Gln Gly Pro Pro Val Pro Gln Phe Gln Pro Gln Lys Ala 20 25 30 Leu Arg Pro Asp Met Gly Tyr Asn Thr Leu Ala Asn Phe Arg Ile 35 40 45 Glu Lys Lys Ile Gly Arg Gly Gln Phe Ser Glu Val Tyr Arg Ala 50 55 60 Ala Cys Leu Leu Asp Gly Val Pro Val Ala Leu Lys Lys Val Gln 65 70 75 Ile Phe Asp Leu Met Asp Ala Lys Ala Arg Ala Asp Cys Ile Lys 80 85 90 Glu Ile Asp Leu Leu Lys Gln Leu Asn His Pro Asn Val Ile Lys 95 100 105 Tyr Tyr Ala Ser Phe Ile Glu Asp Asn Glu Leu Asn Ile Val Leu 110 115 120 Glu Leu Ala Asp Ala Gly Asp Leu Ser Arg Met Ile Lys His Phe 125 130 135 Lys Lys Gln Lys Arg Leu Ile Pro Glu Arg Thr Val Trp Lys Tyr 140 145 150 Phe Val Gln Leu Cys Ser Ala Leu Glu His Met His Ser Arg Arg 155 160 165 Xaa Met His Arg Asp Ile Lys Pro Ala Asn Val Phe Ile Thr Ala 170 175 180 Thr Gly Val Val Lys Leu Gly Asp Leu Gly Leu Gly Arg Phe Phe 185 190 195 Ser Ser Lys Thr Thr Ala Ala His Ser Leu Val Gly Thr Pro Tyr 200 205 210 Tyr Met Ser Pro Glu Arg Ile His Glu Asn Gly Ile Gln Leu Gln 215 220 225 Ile 62 334 PRT Homo sapiens misc_feature Incyte ID No 233678.1.orf2 62 Pro Val Pro Glu Ala Cys Val Thr Leu Asn Leu Pro Thr Ser Gln 1 5 10 15 Ala Ile Pro Ser Leu Leu Lys Ala His Pro Trp Ala Ser Gly Pro 20 25 30 Cys Pro Arg Arg Gly Arg Glu Ala Thr Ala Ser Asp Ala Pro Gly 35 40 45 Arg Pro Leu Pro Ser Pro Leu Pro Ala Gln Val Leu Glu Thr Cys 50 55 60 Met Lys Ser Cys Gly Lys Arg Phe His Asp Glu Val Gly Lys Phe 65 70 75 Arg Phe Leu Asn Glu Leu Ile Lys Val Val Ser Pro Lys Tyr Leu 80 85 90 Gly Ser Arg Thr Ser Glu Lys Val Lys Asn Lys Ile Leu Glu Leu 95 100 105 Leu Tyr Ser Trp Thr Val Gly Leu Pro Glu Glu Val Lys Ile Ala 110 115 120 Glu Ala Tyr Gln Met Leu Lys Lys Gln Gly Ile Val Lys Ser Asp 125 130 135 Pro Lys Leu Pro Asp Asp Thr Thr Phe Pro Leu Pro Pro Pro Arg 140 145 150 Pro Lys Asn Val Ile Phe Glu Asp Glu Glu Lys Ser Lys Met Leu 155 160 165 Ala Arg Leu Leu Lys Ser Ser His Pro Glu Asp Leu Arg Ala Pro 170 175 180 Ile Ser Ser Ser Lys Arg Trp Cys Arg Arg Thr Arg Ser Gly Trp 185 190 195 Arg Arg Ser Arg Arg Gly Val Asn Ala Ile Glu Glu Val Asn Asn 200 205 210 Asn Val Lys Leu Ala His Gly Asp Gly Asp Glu Pro Gln Pro Gly 215 220 225 Arg Arg Thr Ala Gly Ser Ser Glu Asp Leu Met Lys Glu Leu Tyr 230 235 240 Gln Arg Cys Glu Arg Met Arg Pro Thr Leu Phe Arg Leu Ala Ser 245 250 255 Asp Thr Glu Asp Asn Asp Glu Ala Leu Ala Glu Ile Leu Gln Ala 260 265 270 Asn Asp Asn Leu Thr Gln Val Ile Asn Leu Tyr Lys Gln Leu Val 275 280 285 Arg Gly Glu Glu Val Asn Gly Asp Ala Thr Ala Gly Ser Ile Pro 290 295 300 Gly Glu His Leu Gly Pro Ala Gly Ser Leu Arg Pro Gly Ser Pro 305 310 315 Ala Cys Gly His His Leu Pro Ser Tyr Ala His Pro Pro Trp Arg 320 325 330 Ala Gly Gln Pro 63 326 PRT Homo sapiens misc_feature Incyte ID No 312243.1.orf2 63 Gly Pro His Arg Pro Arg Glu Leu Leu Arg Ala Leu Ser Met Arg 1 5 10 15 Ser Arg Ala Pro Arg Gly Ser Asp Val Ala Ala Pro Val Ser Arg 20 25 30 Pro Pro Ser Ser Ser Asp Ala Gly Leu Arg Phe Pro Asp Ser Asn 35 40 45 Gly Leu Leu Gln Thr Pro Arg Trp Asp Glu Pro Gln Arg Val Cys 50 55 60 Ala Leu Glu Gln Ile Cys Gly Val Phe Arg Val Asp Leu Gly His 65 70 75 Met Arg Ser Leu Arg Leu Phe Phe Ser Asp Glu Ala Cys Thr Ser 80 85 90 Gly Gln Leu Val Val Ala Ser Arg Glu Ser Gln Tyr Lys Val Phe 95 100 105 His Phe His His Gly Gly Leu Asp Lys Leu Ser Asp Val Phe Gln 110 115 120 Gln Trp Lys Tyr Cys Thr Glu Met Gln Leu Lys Asp Gln Gln Val 125 130 135 Ala Pro Asp Lys Thr Cys Met Gln Phe Ser Ile Arg Arg Pro Lys 140 145 150 Leu Pro Ser Ser Glu Thr His Pro Glu Glu Ser Met Tyr Lys Arg 155 160 165 Leu Gly Val Ser Ala Trp Leu Asn His Leu Asn Glu Leu Gly Gln 170 175 180 Val Glu Glu Glu Tyr Lys Leu Arg Lys Ala Ile Phe Phe Gly Gly 185 190 195 Ile Asp Val Ser Ile Arg Gly Glu Val Trp Pro Phe Leu Leu Arg 200 205 210 Tyr Tyr Ser His Glu Ser Thr Ser Glu Glu Arg Glu Ala Leu Arg 215 220 225 Leu Gln Lys Arg Lys Glu Tyr Ser Glu Ile Gln Gln Lys Arg Leu 230 235 240 Ser Met Thr Pro Glu Glu His Arg Ala Phe Trp Arg Asn Val Gln 245 250 255 Phe Thr Val Asp Lys Asp Val Val Arg Thr Asp Arg Asn Asn Gln 260 265 270 Phe Phe Arg Gly Glu Asp Asn Pro Asn Val Glu Ser Met Arg Arg 275 280 285 Ile Leu Leu Asn Tyr Ala Val Tyr Asn Pro Ala Val Gly Ile Pro 290 295 300 Lys Gly Cys Arg Thr Trp Trp Arg Pro Ser Trp Pro Arg Ser Trp 305 310 315 Met Ser Gln Thr Pro Ser Gly Ala Leu Trp Val 320 325 64 121 PRT Homo sapiens misc_feature Incyte ID No 425487.3.orf3 64 Pro Phe Leu Ser Leu Cys Tyr Arg Glu Pro Arg Gly Ala Leu Leu 1 5 10 15 Pro His Arg Ser Phe Ser Leu Glu Lys Gly Gly Pro Leu Arg Gly 20 25 30 Leu Pro Ser Gln Gln Val Gly Gly Gly Arg Ser Gly Pro Gly Ser 35 40 45 Pro Pro Phe Phe Leu Leu Phe Leu Val Cys Phe Phe Arg Ala Ala 50 55 60 Leu Ser Leu Leu Trp Glu Lys Glu Arg Lys Val Leu Phe His Leu 65 70 75 Pro Phe Leu Asp Gln Gly Trp Gln Val His Val Pro Phe Leu Glu 80 85 90 Arg Ala Val Leu Ala Gln Gly Pro Leu Ala Val Gly Arg Tyr Glu 95 100 105 Tyr Gly Leu Arg Val Ala Ser Leu Gly Leu Cys Ile Cys Leu Ser 110 115 120 Val 65 109 PRT Homo sapiens misc_feature Incyte ID No 346813.3.j.orf3 65 His Ser Lys Lys Lys Ile Ser Val Ser Val Lys Asn Cys Ile Tyr 1 5 10 15 Val Arg Cys Val Asn Thr Gly Leu Val Ser Phe Gly Leu Leu Lys 20 25 30 Lys Lys Ile Lys Lys Ile Leu Phe Gly Gly Leu Val Val Leu Gly 35 40 45 Lys Asn Cys Ile Met Val Pro Gln Lys Val Thr Trp Trp Ser Ser 50 55 60 Asn Tyr Thr Glu Arg Asn Pro Phe Ser Lys Phe Pro Xaa Xaa Xaa 65 70 75 Thr Val Trp Ala His Pro Glu Leu His Arg Asp Trp Xaa Ala Pro 80 85 90 Thr Gly Leu Tyr Ala Glu Leu Xaa Leu Ser Ser Leu Ile Ser Gly 95 100 105 Gln Xaa Ala Val 66 64 PRT Homo sapiens misc_feature Incyte ID No 006861.1.j.orf2 66 Thr Val Glu Lys Thr Leu Asp Lys Lys Gln Ile Arg Val Ile Phe 1 5 10 15 Leu Phe Glu Leu Arg Met Gly Cys Lys Ala Val Glu Thr Thr Arg 20 25 30 Gln His Gln His His Ile Gly Pro Arg Ser Arg Trp Glu Pro Leu 35 40 45 Asn Glu His Thr Val Gln Cys Trp Val Lys Lys Phe Tyr Arg Leu 50 55 60 Gly Leu Glu Ala 67 108 PRT Homo sapiens misc_feature Incyte ID No 028008.3.j.orf3 67 Arg Glu Thr Glu Lys Leu Asp Leu Arg Ala Leu Leu Cys Gln Leu 1 5 10 15 Phe Tyr Ser Phe Phe Lys Ser Leu Val Gly Lys Asp Val Val Val 20 25 30 Glu Leu Lys Asn Asp Leu Ser Ile Cys Gly Thr Leu His Ser Val 35 40 45 Asp Gln Tyr Leu Asn Ile Lys Leu Thr Asp Ile Ser Val Thr Asp 50 55 60 Pro Glu Lys Tyr Pro His Met Leu Ser Val Lys Asn Cys Phe Ile 65 70 75 Arg Gly Ser Val Val Arg Tyr Val Gln Leu Pro Ala Asp Glu Val 80 85 90 Asp Thr Gln Leu Leu Gln Asp Ala Ala Arg Lys Glu Ala Leu Gln 95 100 105 Gln Lys Gln 68 322 PRT Homo sapiens misc_feature Incyte ID No 346078.5.j.orf1 68 Thr Glu Glu Lys Met Ser Leu Tyr Asp Asp Leu Gly Val Glu Thr 1 5 10 15 Ser Asp Ser Lys Thr Glu Gly Trp Ser Lys Asn Phe Lys Leu Leu 20 25 30 Gln Ser Gln Leu Gln Val Lys Lys Ala Ala Leu Thr Gln Ala Lys 35 40 45 Ser Gln Arg Thr Lys Gln Ser Thr Val Leu Ala Pro Val Ile Asp 50 55 60 Leu Lys Arg Gly Gly Ser Ser Asp Asp Arg Gln Ile Val Asp Thr 65 70 75 Pro Pro His Val Ala Ala Gly Leu Lys Asp Pro Val Pro Ser Gly 80 85 90 Phe Ser Ala Gly Glu Val Leu Ile Pro Leu Ala Asp Glu Tyr Asp 95 100 105 Pro Met Phe Pro Asn Asp Tyr Glu Lys Val Val Lys Arg Gln Arg 110 115 120 Glu Glu Arg Gln Arg Gln Arg Glu Leu Glu Arg Gln Lys Glu Ile 125 130 135 Glu Glu Arg Glu Lys Arg Arg Lys Asp Arg His Glu Ala Ser Gly 140 145 150 Phe Ala Arg Arg Pro Asp Pro Asp Ser Asp Glu Asp Glu Asp Tyr 155 160 165 Glu Arg Glu Arg Arg Lys Arg Ser Met Gly Gly Val Ala Ile Ala 170 175 180 Pro Pro Thr Ser Leu Val Glu Lys Asp Lys Glu Leu Pro Arg Asp 185 190 195 Phe Pro Tyr Glu Glu Asp Ser Arg Pro Arg Ser Gln Ser Ser Lys 200 205 210 Ala Ala Ile Pro Pro Pro Val Tyr Glu Glu Gln Asp Arg Pro Arg 215 220 225 Ser Pro Thr Gly Pro Ser Asn Ser Phe Leu Ala Asn Met Gly Gly 230 235 240 Thr Val Ala His Lys Ile Met Gln Lys Tyr Gly Phe Arg Glu Gly 245 250 255 Gln Gly Leu Gly Lys His Glu Gln Gly Leu Ser Thr Ala Leu Ser 260 265 270 Val Glu Lys Thr Ser Lys Arg Gly Gly Lys Ile Ile Val Gly Asp 275 280 285 Ala Thr Glu Lys Gly Val Ser Pro Gly Lys Arg Val Thr Arg Gly 290 295 300 Lys Gly Leu Ala Pro Ser Ile Ser Asp Met Ala Ser Leu Asp Pro 305 310 315 His Val Ser Ala Gly Gly Gln 320 69 66 PRT Homo sapiens misc_feature Incyte ID No 394637.1.j.orf3 69 Ile Arg Glu Ile Phe Leu Phe Lys Leu Thr Met Gly Arg Lys Thr 1 5 10 15 Ala Glu Thr Thr Cys Asn Ile Asn Met His Leu Ala Gln Glu Leu 20 25 30 Leu Met Asn Val Gln Cys Ser Gly Gly Ser Arg Ser Phe Ala Lys 35 40 45 Asp Thr Arg Ala Leu Arg Met Arg Ser Val Val Ala Gly His Trp 50 55 60 Lys Leu Thr Thr Thr Asn 65 70 107 PRT Homo sapiens misc_feature Incyte ID No 222429.3.orf1 70 Gly Glu Glu Leu Gln Pro Trp Pro Met Asp Leu Ile Gly Phe Gly 1 5 10 15 Tyr Ala Ala Leu Val Thr Phe Gly Ser Ile Phe Gly Tyr Lys Arg 20 25 30 Arg Gly Gly Val Pro Ser Leu Ile Ala Gly Leu Phe Val Gly Cys 35 40 45 Leu Ala Gly Tyr Gly Ala Tyr Arg Val Ser Asn Asp Lys Arg Asp 50 55 60 Val Lys Val Ser Leu Phe Thr Ala Phe Phe Leu Ala Thr Ile Met 65 70 75 Gly Val Arg Phe Lys Arg Ser Lys Lys Ile Met Pro Ala Gly Leu 80 85 90 Val Ala Gly Leu Ser Leu Met Met Ile Leu Arg Leu Val Leu Leu 95 100 105 Leu Leu 71 250 PRT Homo sapiens misc_feature Incyte ID No 366739.2.orf1 71 Thr Ser Ser Pro Cys Val Trp Leu Arg Gly Arg Pro Ala Ala Leu 1 5 10 15 Ala Ala Ser Glu Ile Thr Gly Leu Ser Thr Ala Val Leu Ala Ala 20 25 30 His Gly Arg Gln Cys Phe Asp Asp Asn Leu Ala Asn Leu Leu Leu 35 40 45 Ala Phe Leu Arg Arg Gln His Gln Pro Trp Cys Leu Val Ala His 50 55 60 Asn Gly Asp Arg Tyr Asp Phe Pro Leu Leu Gln Ala Glu Leu Ala 65 70 75 Met Leu Gly Leu Thr Ser Ala Leu Asp Gly Ala Phe Cys Val Asp 80 85 90 Ser Ile Thr Ala Leu Lys Ala Leu Glu Arg Ala Ser Ser Pro Ser 95 100 105 Glu His Gly Pro Arg Lys Ser Tyr Ser Leu Gly Ser Ile Tyr Thr 110 115 120 Arg Leu Tyr Gly Gln Ser Pro Pro Asp Ser His Thr Ala Glu Gly 125 130 135 Asp Val Leu Ala Leu Leu Ser Ile Cys Gln Trp Arg Pro Gln Ala 140 145 150 Leu Leu Arg Trp Val Asp Ala His Ala Arg Pro Phe Gly Thr Ile 155 160 165 Arg Pro Met Tyr Gly Val Thr Ala Ser Ala Arg Thr Lys Pro Arg 170 175 180 Pro Ser Ala Val Thr Thr Thr Ala His Leu Ala Thr Thr Arg Asn 185 190 195 Thr Ser Pro Ser Leu Gly Glu Ser Arg Gly Thr Lys Asp Leu Pro 200 205 210 Pro Val Lys Asp Pro Gly Ala Leu Ser Arg Glu Gly Leu Leu Ala 215 220 225 Pro Leu Gly Leu Leu Ala Ile Leu Thr Leu Ala Val Ala Thr Leu 230 235 240 Tyr Gly Leu Ser Leu Ala Thr Pro Gly Glu 245 250 72 197 PRT Homo sapiens misc_feature Incyte ID No 474635.6.orf3 72 Pro Ala Arg His Gly Val Arg Arg Arg Gly Pro Gly Glu Val Ala 1 5 10 15 Pro Thr Leu Arg Ser Glu Val Leu Leu Pro Ser Pro Ser Leu Pro 20 25 30 Thr Ser Cys Ser Leu Leu Arg Pro Ala Glu Leu Ala Asp Gly Ala 35 40 45 Ala His Gly Ser Val Gly Ser Gln Ala Val Ala Arg Arg Met Asp 50 55 60 Gly Asp Ser Arg Asp Gly Gly Gly Gly Lys Asp Ala Thr Gly Ser 65 70 75 Glu Asp Tyr Glu Asn Leu Pro Thr Ser Ala Ser Val Ser Thr His 80 85 90 Met Thr Ala Gly Ala Met Ala Gly Ile Leu Glu His Ser Val Met 95 100 105 Tyr Pro Val Asp Ser Val Lys Thr Arg Met Gln Ser Leu Ser Pro 110 115 120 Asp Pro Lys Ala Gln Tyr Thr Ser Ile Tyr Gly Ala Leu Lys Lys 125 130 135 Ile Met Arg Thr Glu Gly Phe Trp Arg Pro Leu Arg Gly Val Asn 140 145 150 Val Met Ile Met Gly Ala Gly Pro Ala His Ala Met Tyr Phe Ala 155 160 165 Cys Tyr Glu Asn Met Lys Arg Thr Leu Asn Asp Val Phe His His 170 175 180 Gln Gly Asn Ser His Leu Ala Asn Gly Ile Leu Lys Ala Phe Val 185 190 195 Trp Ser 73 133 PRT Homo sapiens misc_feature Incyte ID No 228470.1.j.orf3 73 Gln Lys Arg Arg Lys Arg Arg Xaa Xaa Lys Ile Met Lys Thr Ile 1 5 10 15 Gln Pro Lys Met His Asn Ser Ile Ser Trp Ala Ile Phe Thr Gly 20 25 30 Leu Ala Ala Leu Cys Leu Phe Gln Gly Val Pro Val Arg Arg Glu 35 40 45 Asp Ala Thr Phe Pro Lys Ala Met Asp Asn Val Thr Val Arg Gln 50 55 60 Gly Glu Ser Ala Thr Leu Arg Cys Thr Ile Asp Asn Arg Val Thr 65 70 75 Arg Val Ala Trp Leu Asn Arg Ser Thr Ile Leu Tyr Ala Gly Asn 80 85 90 Asp Lys Trp Cys Leu Asp Pro Arg Val Val Leu Leu Ser Asn Thr 95 100 105 Gln Thr His Tyr Ser Ile Glu Ile Gln Asn Val Asp Val Tyr Asp 110 115 120 Glu Gly Pro Tyr Thr Cys Ser Val Gln Thr Asp Asn His 125 130 74 516 PRT Homo sapiens misc_feature Incyte ID No 407090.5.j.orf1 74 Ser Leu Leu Ile Val Asn Leu Pro Leu Thr Pro Val Gly Ser Glu 1 5 10 15 Asp Ala Asp Ser Ala Ser Glu Leu Ala Asp Ser Glu Gly Gly Glu 20 25 30 Glu Tyr Asn Ala Met Met Lys Asn Cys Leu Arg Val Asn Leu Thr 35 40 45 Leu Ala Asp Leu Glu Gln Leu Ala Gly Ser Asp Leu Lys Val Pro 50 55 60 Asn Glu Asp Thr Lys Ser Asp Gly Pro Glu Thr Thr Thr Gln Cys 65 70 75 Lys Phe Asp Arg Cys Ser Lys Ser Pro Lys Thr Pro Thr Gly Leu 80 85 90 Arg Arg Gly Arg Gln Cys Ile Arg Pro Ala Glu Ile Val Ala Ser 95 100 105 Leu Leu Glu Gly Glu Glu Asn Thr Cys Gly Lys Gln Lys Pro Lys 110 115 120 Glu Asn Asn Leu Lys Pro Lys Phe Gln Ala Phe Lys Gly Val Gly 125 130 135 Cys Leu Tyr Glu Lys Glu Ser Met Lys Lys Ser Leu Lys Asp Ser 140 145 150 Val Ala Ser Asn Asn Lys Asp Gln Asn Ser Met Lys His Glu Asp 155 160 165 Pro Ser Ile Ile Ser Met Glu Asp Gly Ser Pro Tyr Val Asn Gly 170 175 180 Ser Leu Gly Glu Val Thr Pro Cys Gln His Ala Lys Lys Ala Asn 185 190 195 Gly Pro Asn Tyr Ile Gln Pro Gln Lys Arg Gln Thr Thr Phe Glu 200 205 210 Ser Gln Asp Arg Lys Ala Val Ser Pro Ser Ser Ser Glu Lys Arg 215 220 225 Ser Lys Asn Pro Ile Ser Arg Pro Leu Glu Gly Lys Lys Ser Leu 230 235 240 Ser Leu Ser Ala Lys Thr His Asn Ile Gly Phe Asp Lys Asp Ser 245 250 255 Cys His Ser Thr Thr Lys Thr Glu Ala Ser Gln Glu Glu Arg Ser 260 265 270 Asp Ser Ser Gly Leu Thr Ser Leu Lys Lys Ser Pro Lys Val Ser 275 280 285 Ser Lys Asp Thr Arg Glu Ile Lys Thr Asp Phe Ser Leu Ser Ile 290 295 300 Ser Asn Ser Ser Asp Val Ser Ala Lys Asp Lys His Ala Glu Asp 305 310 315 Asn Glu Lys Arg Leu Ala Ala Leu Glu Ala Arg Gln Lys Ala Lys 320 325 330 Glu Val Gln Lys Lys Leu Val His Asn Ala Leu Ala Asn Leu Asp 335 340 345 Gly His Pro Glu Asp Lys Pro Thr His Ile Ile Phe Gly Ser Asp 350 355 360 Ser Glu Cys Glu Thr Glu Glu Thr Ser Thr Gln Glu Gln Ser His 365 370 375 Pro Gly Glu Glu Trp Val Lys Glu Ser Met Gly Lys Thr Ser Gly 380 385 390 Lys Leu Phe Asp Ser Ser Asp Asp Asp Glu Ser Asp Ser Glu Asp 395 400 405 Asp Ser Asn Arg Phe Lys Ile Lys Pro Gln Phe Glu Gly Arg Ala 410 415 420 Gly Gln Lys Leu Met Asp Leu Gln Ser His Phe Gly Thr Asp Asp 425 430 435 Arg Phe Arg Met Asp Ser Arg Phe Leu Glu Thr Asp Ser Glu Glu 440 445 450 Glu Gln Glu Glu Val Asn Glu Lys Lys Thr Ala Glu Glu Glu Glu 455 460 465 Xaa Ala Glu Glu Xaa Xaa Lys Ala Leu Asn Val Val Gln Ser Val 470 475 480 Leu Gln Ile Asn Leu Ser Asn Ser Thr Asn Arg Gly Xaa Val Ala 485 490 495 Ala Lys Lys Phe Lys Asp Ile Ile His Tyr Asp Pro Xaa Lys Gln 500 505 510 Asp His Ala Thr Tyr Glu 515 75 142 PRT Homo sapiens misc_feature Incyte ID No 068194.1.j.orf1 75 Pro Lys Ser Leu Glu Glu Ala Thr Pro Ser Lys Glu Gly Asp Ile 1 5 10 15 Leu Lys Pro Glu Glu Glu Thr Met Glu Phe Pro Glu Gly Asp Lys 20 25 30 Val Lys Val Ile Leu Ser Lys Glu Asp Phe Glu Ala Ser Leu Lys 35 40 45 Glu Ala Gly Glu Arg Leu Val Ala Val Asp Phe Ser Ala Thr Trp 50 55 60 Cys Gly Pro Cys Arg Thr Ile Arg Pro Phe Phe His Ala Leu Ser 65 70 75 Val Lys His Glu Asp Val Val Phe Leu Glu Val Asp Ala Asp Asn 80 85 90 Cys Glu Glu Val Val Arg Glu Cys Ala Ile Met Cys Val Pro Thr 95 100 105 Phe Gln Phe Tyr Xaa Lys Glu Glu Lys Val Asp Glu Leu Cys Gly 110 115 120 Ala Leu Lys Glu Lys Leu Glu Ala Val Ile Ala Glu Leu Lys Xaa 125 130 135 Asn Met Tyr Ser Glu Asn Lys 140 76 111 PRT Homo sapiens misc_feature Incyte ID No 411449.2.orf1 76 Pro Ala Arg Ser Gln Ala Ala Leu Glu Pro Cys Pro Lys Gly Ser 1 5 10 15 Lys Pro Leu Phe Tyr Ile His Ser Leu Gln Arg Leu Leu Gln Ser 20 25 30 Pro Pro Ser Ser Asp Asn Val Leu Val Val Phe Lys Tyr Ile Val 35 40 45 Ala Tyr Asp Pro His Asn Pro Val Arg Gln Trp Gly Asp Gly Glu 50 55 60 Thr Lys Thr His Ser Gly Met Xaa Tyr Leu Phe Tyr Gly His Val 65 70 75 Ala Cys Ala Val Asn Cys Ala Phe Cys Cys Ser Ala Ala Thr Arg 80 85 90 Arg Cys Asn Ser Ala Ser Ser Ala Ser Pro Ser Ser Ala Ile Val 95 100 105 Arg Leu Gln Ala Arg His 110 77 128 PRT Homo sapiens misc_feature Incyte ID No 018549.2.orf2 77 Cys Leu Arg Gln Ala Gly Ala Ser Leu Leu Arg Lys Leu Trp Pro 1 5 10 15 Glu Ala Gln Ile Arg Asn Thr Met Ala Leu Leu Thr Ala Glu Thr 20 25 30 Phe Arg Leu Gln Phe Asn Asn Lys Arg Leu Leu Arg Arg Pro Tyr 35 40 45 Tyr Pro Arg Lys Ala Leu Leu Cys Tyr Gln Leu Thr Pro Gln Asn 50 55 60 Gly Ser Thr Pro Thr Arg Gly Tyr Phe Glu Asn Lys Lys Lys Cys 65 70 75 His Ala Glu Ile Cys Phe Ile Asn Glu Ile Lys Ser Met Gly Leu 80 85 90 Asp Glu Thr His Ala Tyr Gln Val Thr Cys Tyr Leu Thr Trp Ser 95 100 105 Pro Cys Ser Ser Cys Ala Trp Glu Leu Val Asp Phe Ile Xaa Ala 110 115 120 His Asp His Leu Asn Leu Gly Ile 125 78 351 PRT Homo sapiens misc_feature Incyte ID No 236043.3.orf3 78 Val Pro His Ser Gly Glu Gly Val Gly Ala Thr Met Ser Ser Tyr 1 5 10 15 Gln Lys Glu Leu Glu Lys Tyr Arg Asp Ile Asp Glu Asp Glu Ile 20 25 30 Leu Arg Thr Leu Ser Pro Glu Glu Leu Glu Gln Leu Asp Cys Glu 35 40 45 Leu Gln Glu Met Asp Pro Glu Asn Met Leu Leu Pro Ala Gly Leu 50 55 60 Arg Gln Arg Asp Gln Thr Lys Lys Ser Pro Thr Gly Pro Leu Asp 65 70 75 Arg Glu Ala Leu Leu Gln Tyr Leu Glu Gln Gln Ala Leu Glu Val 80 85 90 Lys Glu Arg Asp Asp Leu Val Pro Phe Thr Gly Glu Lys Lys Gly 95 100 105 Lys Pro Tyr Ile Gln Pro Lys Arg Glu Ile Pro Ala Glu Glu Gln 110 115 120 Ile Thr Leu Glu Pro Glu Leu Glu Glu Ala Leu Ala His Ala Thr 125 130 135 Asp Ala Glu Met Cys Asp Ile Ala Ala Ile Leu Asp Met Tyr Thr 140 145 150 Leu Met Ser Asn Lys Gln Tyr Tyr Asp Ala Leu Cys Ser Gly Glu 155 160 165 Ile Cys Asn Thr Glu Gly Ile Ser Ser Val Val Gln Pro Asp Lys 170 175 180 Tyr Lys Pro Val Pro Asp Glu Pro Pro Asn Pro Thr Asn Ile Glu 185 190 195 Glu Ile Leu Lys Arg Val Arg Ser Asn Asp Lys Glu Leu Glu Glu 200 205 210 Val Asn Leu Asn Asn Ile Gln Asp Ile Pro Ile Pro Met Leu Ser 215 220 225 Glu Leu Cys Glu Ala Met Lys Ala Asn Thr Tyr Val Arg Ser Phe 230 235 240 Ser Leu Val Ala Thr Arg Ser Gly Asp Pro Ile Ala Asn Ala Val 245 250 255 Ala Asp Met Leu Arg Glu Asn Arg Ser Leu Gln Ser Leu Asn Ile 260 265 270 Glu Ser Asn Phe Ile Ser Ser Thr Gly Leu Met Ala Val Leu Lys 275 280 285 Ala Val Arg Glu Asn Ala Thr Leu Thr Glu Leu Arg Val Asp Asn 290 295 300 Gln Arg Gln Trp Pro Gly Asp Ala Val Glu Met Glu Met Ala Thr 305 310 315 Val Leu Glu Gln Cys Pro Ser Ile Val Arg Phe Gly Tyr His Phe 320 325 330 Thr Gln Gln Gly Pro Arg Ala Arg Ala Ala Gln Ala Met Thr Arg 335 340 345 Asn Asn Glu Leu Arg Glu 350 79 146 PRT Homo sapiens misc_feature Incyte ID No 445433.2.orf2 79 Asn Ser Asn Leu Val Tyr Tyr Asn Phe Ile His Arg Ile Cys Gln 1 5 10 15 Leu Leu Ser Asp Tyr Lys Glu Lys Gln Ile Leu Lys Val Ser Ser 20 25 30 Glu Asn Ser Asn Pro Glu Gln Asp Leu Lys Leu Thr Ser Glu Glu 35 40 45 Glu Ser Gln Arg Leu Lys Gly Ser Glu Asn Ser Gln Pro Glu Glu 50 55 60 Met Ser Gln Glu Pro Glu Ile Asn Lys Gly Gly Asp Arg Lys Val 65 70 75 Glu Glu Glu Met Lys Lys His Gly Ser Thr His Met Gly Phe Pro 80 85 90 Glu Asn Leu Pro Asn Gly Ala Thr Ala Asp Asn Gly Asp Asp Gly 95 100 105 Leu Ile Pro Pro Arg Lys Ser Arg Thr Pro Glu Ser Gln Gln Phe 110 115 120 Pro Asp Thr Glu Asn Glu Gln Tyr His Arg Asp Phe Ser Gly His 125 130 135 Pro Asn Phe Pro Thr Thr Leu Pro Ile Lys Gln 140 145 80 345 PRT Homo sapiens misc_feature Incyte ID No 344630.7.j.orf3 80 Gly Cys Thr Ser Ser Ser Thr Pro Pro Ser Gln Gly Thr Ser Ala 1 5 10 15 Ser Trp Glu Ser Gln Arg Glu Phe Val Arg Arg Phe Arg Gly Gln 20 25 30 Ala Asp Cys Arg Gln Ala Leu Pro Leu Leu Ala Ser Ala Cys Pro 35 40 45 Gly Trp Ile Cys Tyr Ala Glu Lys Thr His Gly Ser Phe Ile Leu 50 55 60 Pro His Ile Ser Thr Ala Arg Ser Pro Gln Gln Val Met Gly Ser 65 70 75 Leu Val Lys Asp Phe Phe Ala Gln Gln Gln His Leu Thr Pro Asp 80 85 90 Lys Ile Tyr His Val Thr Val Met Pro Cys Tyr Asp Lys Lys Leu 95 100 105 Glu Ala Ser Arg Pro Asp Phe Phe Asn Gln Glu His Gln Thr Arg 110 115 120 Asp Val Asp Cys Val Leu Thr Thr Gly Glu Val Phe Arg Leu Leu 125 130 135 Glu Glu Glu Gly Val Ser Leu Pro Asp Leu Glu Pro Ala Pro Leu 140 145 150 Asp Ser Leu Cys Ser Gly Ala Ser Ala Glu Glu Pro Thr Ser His 155 160 165 Arg Gly Gly Gly Ser Gly Gly Tyr Leu Glu His Val Phe Arg His 170 175 180 Ala Ala Arg Glu Leu Phe Gly Ile His Val Ala Glu Val Thr Tyr 185 190 195 Lys Pro Leu Arg Asn Lys Asp Phe Gln Glu Val Thr Leu Glu Lys 200 205 210 Glu Gly Gln Val Leu Leu His Phe Ala Met Ala Tyr Gly Phe Arg 215 220 225 Asn Ile Gln Asn Leu Val Gln Arg Leu Lys Arg Gly Arg Cys Pro 230 235 240 Tyr His Tyr Val Glu Val Met Ala Cys Pro Ser Gly Cys Leu Asn 245 250 255 Gly Gly Gly Gln Leu Gln Ala Pro Asp Arg Pro Ser Arg Glu Leu 260 265 270 Leu Gln His Val Glu Arg Leu Tyr Gly Met Val Arg Ala Glu Ala 275 280 285 Pro Glu Asp Ala Pro Gly Val Gln Glu Leu Tyr Thr His Trp Leu 290 295 300 Gln Gly Thr Asp Ser Glu Cys Ala Gly Arg Leu Leu His Thr Gln 305 310 315 Tyr His Ala Val Glu Lys Ala Ser Thr Gly Leu Val His Pro Val 320 325 330 Val Gly Ala Ala Gly Pro Gly Leu Pro Gly Gly Arg Val His Val 335 340 345 81 690 PRT Homo sapiens misc_feature Incyte ID No 257121.2.orf2 81 Leu Val Ile Thr Asp Leu Val Trp Ile Ala Tyr Arg Gln Tyr Leu 1 5 10 15 Arg Ile Glu Ile Ser Glu Ser Arg Val Asn Ile Ser Cys Pro Glu 20 25 30 Cys Thr Glu Arg Phe Asn Pro His Asp Ile Arg Leu Ile Leu Ser 35 40 45 Asp Asp Val Leu Met Glu Lys Tyr Glu Glu Phe Met Leu Arg Arg 50 55 60 Trp Leu Val Ala Asp Pro Asp Cys Arg Trp Cys Pro Ala Pro Asp 65 70 75 Cys Gly Tyr Ala Val Ile Ala Phe Gly Cys Ala Ser Cys Pro Lys 80 85 90 Leu Thr Cys Gly Arg Glu Gly Cys Gly Thr Glu Phe Cys Tyr His 95 100 105 Cys Lys Gln Ile Trp His Pro Asn Gln Thr Cys Asp Ala Ala Arg 110 115 120 Gln Glu Arg Ala Gln Ser Leu Arg Leu Arg Thr Ile Arg Ser Ser 125 130 135 Ser Ile Ser Tyr Ser Gln Glu Ser Gly Ala Ala Ala Asp Asp Ile 140 145 150 Lys Pro Cys Pro Arg Cys Ala Ala Tyr Ile Ile Lys Met Asn Asp 155 160 165 Gly Ser Cys Asn His Met Thr Cys Ala Val Cys Gly Cys Glu Phe 170 175 180 Cys Trp Leu Cys Met Lys Glu Ile Ser Asp Leu His Tyr Leu Ser 185 190 195 Pro Ser Gly Cys Thr Phe Trp Gly Lys Lys Pro Trp Ser Arg Lys 200 205 210 Lys Lys Ile Leu Trp Gln Leu Gly Thr Leu Val Gly Ala Pro Val 215 220 225 Gly Ile Ala Leu Ile Ala Gly Ile Ala Ile Pro Ala Met Ile Ile 230 235 240 Gly Ile Pro Val Tyr Val Gly Arg Lys Ile His Asn Arg Tyr Glu 245 250 255 Gly Lys Asp Val Ser Lys His Lys Arg Asn Leu Ala Ile Ala Gly 260 265 270 Gly Val Thr Leu Ser Val Ile Val Ser Pro Val Val Ala Ala Val 275 280 285 Thr Val Gly Ile Gly Val Pro Ile Met Leu Ala Tyr Val Tyr Gly 290 295 300 Val Val Pro Ile Ser Leu Cys Arg Ser Gly Gly Cys Gly Val Ser 305 310 315 Ala Gly Asn Gly Lys Gly Val Arg Ile Glu Phe Asp Asp Glu Asn 320 325 330 Asp Ile Asn Val Gly Gly Thr Asn Thr Ala Val Asp Thr Thr Ser 335 340 345 Val Ala Glu Ala Arg His Asn Pro Ser Ile Gly Glu Gly Ser Val 350 355 360 Gly Gly Leu Thr Gly Ser Leu Ser Ala Ser Gly Ser His Met Asp 365 370 375 Arg Ile Gly Ala Ile Arg Asp Asn Leu Ser Xaa Thr Ala Ser Thr 380 385 390 Met Ala Leu Ala Gly Ala Ser Ile Thr Gly Ser Leu Ser Gly Ser 395 400 405 Ala Met Val Asn Cys Phe Asn Arg Leu Glu Val Gln Ala Asp Val 410 415 420 Gln Lys Glu Arg Tyr Ser Leu Ser Gly Glu Ser Gly Thr Val Ser 425 430 435 Leu Gly Thr Val Ser Asp Asn Ala Ser Thr Lys Ala Met Ala Gly 440 445 450 Ser Ile Leu Asn Ser Tyr Ile Pro Leu Asp Lys Glu Gly Asn Ser 455 460 465 Met Glu Val Gln Val Asp Ile Glu Ser Lys Pro Ser Lys Phe Arg 470 475 480 His Asn Ser Gly Ser Ser Ser Val Asp Asp Gly Ser Ala Thr Arg 485 490 495 Ser His Ala Gly Gly Ser Ser Ser Gly Leu Pro Glu Gly Lys Ser 500 505 510 Ser Ala Thr Lys Trp Ser Lys Glu Ala Thr Ala Gly Lys Lys Ser 515 520 525 Lys Ser Gly Lys Leu Arg Lys Lys Gly Asn Met Lys Ile Asn Glu 530 535 540 Thr Arg Glu Asp Met Asp Ala Gln Leu Leu Glu Gln Gln Ser Thr 545 550 555 Asn Ser Ser Glu Phe Glu Ala Pro Ser Leu Ser Asp Ser Met Pro 560 565 570 Ser Val Ala Asp Ser His Ser Ser His Phe Ser Glu Phe Ser Cys 575 580 585 Ser Asp Leu Glu Ser Met Lys Thr Ser Cys Ser His Gly Ser Ser 590 595 600 Asp Tyr His Thr Arg Phe Ala Thr Val Asn Ile Leu Pro Glu Val 605 610 615 Glu Asn Asp Arg Leu Glu Asn Ser Pro His Gln Cys Ser Ile Ser 620 625 630 Val Val Thr Gln Thr Ala Ser Cys Ser Glu Val Ser Gln Leu Asn 635 640 645 His Ile Ala Glu Glu His Gly Asn Asn Gly Ile Lys Pro Asn Val 650 655 660 Asp Leu Tyr Phe Gly Asp Ala Leu Lys Glu Thr Asn Asn Asn His 665 670 675 Ser His Gln Thr Met Glu Leu Lys Val Ala Ile Gln Thr Glu Ile 680 685 690 82 129 PRT Homo sapiens misc_feature Incyte ID No 243794.1.j.orf3 82 Asp Arg Ser Arg Ser Pro Arg Ser Ser Lys Arg Ala Pro Ser Ser 1 5 10 15 Leu Gly Thr Ser Gln Thr Asp Met Ser Lys Leu Arg Val Thr Gly 20 25 30 Gly Asn Thr Glu Val Leu Thr Thr Gly Phe Ile Glu Gly Leu Arg 35 40 45 Ala Arg Ser Met Pro Asn Ile Gly Tyr Gly Arg Asn Lys Lys Thr 50 55 60 Lys His Ile Leu Pro Ser Gly Phe Trp Lys Phe Leu Val His Asn 65 70 75 Val Lys Glu Leu Glu Val Leu Leu Val Ser Asn Lys Ser Tyr Cys 80 85 90 Val Glu Ile Thr His Asp Val Ser Ser Lys Asn Cys Lys Ala Ile 95 100 105 Leu Glu Arg Ala Ala Gln Val Val Ile Arg Val Thr Asn Ala Asn 110 115 120 Ala Ser Leu His Ser Ala Glu Ser Glu 125 83 138 PRT Homo sapiens misc_feature Incyte ID No 442085.1.j.orf2 83 Thr Met Ala Asp Ser Lys Ala Thr Ser Ala Val Thr Leu Arg Thr 1 5 10 15 Arg Lys Phe Met Thr Asn Arg Leu Leu Ala Arg Lys Gln Phe Val 20 25 30 Leu Glu Val Ile His Pro Gly Arg Ala Asn Val Ser Lys Ala Glu 35 40 45 Leu Lys Glu Arg Leu Ala Lys Ala Tyr Glu Val Lys Asp Pro Asn 50 55 60 Thr Ile Phe Val Phe Lys Phe Arg Thr His Phe Gly Gly Gly Lys 65 70 75 Ser Thr Gly Phe Gly Leu Ile Tyr Asp Asn Leu Glu Ala Ala Lys 80 85 90 Lys Phe Glu Pro Lys Tyr Arg Leu Ile Arg Asn Gly Leu Ala Thr 95 100 105 Lys Val Glu Lys Ser Arg Lys Gln Met Lys Glu Arg Lys Asn Arg 110 115 120 Ala Lys Lys Ile Arg Gly Val Lys Lys Thr Lys Ala Gly Asp Ala 125 130 135 Lys Lys Lys 84 133 PRT Homo sapiens misc_feature Incyte ID No 370661.3.j.orf1 84 Arg Glu Ser Ala Val Cys Ala Glu Ala Met Ala Ala Ala Ala Pro 1 5 10 15 Val Ala Ala Asp Asp Asp Glu Arg Arg Arg Arg Pro Gly Ala Ala 20 25 30 Leu Glu Asp Ser Arg Ser Gln Glu Gly Ala Asn Gly Glu Ala Glu 35 40 45 Ser Gly Glu Leu Ser Arg Leu Arg Ala Glu Leu Gly Arg Arg Pro 50 55 60 Gly Arg Asn Gly Asn His Glu Gly Cys Gly Arg Gly Glu Arg Glu 65 70 75 His Glu Gly Arg Gly Cys Gly Cys Gly Ala Arg Gln Cys Gln Glu 80 85 90 Glu Val Ala Ser Leu Gln Ala Ile Leu Lys Asp Ser Ile Ser Ser 95 100 105 Tyr Glu Ala Gln Ile Thr Ala Leu Lys Gln Glu Arg Xaa Ser Ser 110 115 120 Ser Arg Thr Val Arg Arg Arg Ser Gly Ser Trp Ala Ala 125 130 85 271 PRT Homo sapiens misc_feature Incyte ID No 427939.17.j.orf1 85 Arg His Tyr Lys Arg Val Arg Val Thr Tyr Lys Glu Ser Leu Ile 1 5 10 15 Gly Arg Arg Asp Met His Gly Arg Lys Asp Asp Ala Gln Lys Gln 20 25 30 Pro Val Lys Asn Gln Leu Gly Leu Asn Pro Gln Ser His Leu Pro 35 40 45 Glu Leu Gln Leu Phe Gln Ala Glu Gly Lys Ile Tyr Lys Tyr Asp 50 55 60 His Met Glu Lys Ser Val Asn Ser Ser Ser Leu Val Ser Pro Pro 65 70 75 Gln Arg Ile Ser Ser Thr Val Lys Thr His Ile Ser His Thr Tyr 80 85 90 Glu Cys Asn Phe Val Asp Ser Leu Phe Thr Gln Lys Glu Lys Ala 95 100 105 Asn Ile Gly Thr Glu His Tyr Lys Cys Asn Glu Arg Gly Lys Ala 110 115 120 Phe His Gln Gly Leu His Phe Thr Ile His Gln Ile Ile His Thr 125 130 135 Lys Glu Thr Gln Phe Lys Cys Asp Ile Cys Gly Lys Ile Phe Asn 140 145 150 Lys Lys Ser Asn Leu Ala Ser His Gln Arg Ile His Thr Gly Glu 155 160 165 Lys Pro Tyr Lys Cys Asn Glu Cys Gly Lys Val Phe His Asn Met 170 175 180 Ser His Leu Ala Gln His Arg Arg Ile His Thr Gly Glu Lys Pro 185 190 195 Tyr Lys Cys Asn Glu Cys Gly Lys Val Phe Asn Gln Ile Ser His 200 205 210 Leu Ala Gln Leu Ser Lys Glu Phe Ile Pro Glu Arg Asn Leu Ile 215 220 225 Asn Val Met Asn Val Glu Arg Ser Ser Ile Lys Phe His Thr Leu 230 235 240 His Asn Ile Gly Gln Phe Ile Leu Glu Lys Asn Leu Thr Asn Val 245 250 255 Thr Asn Val Ala Arg Cys Ser Val Ala Ile Pro Thr Leu Tyr Asn 260 265 270 Ile 86 45 PRT Homo sapiens misc_feature Incyte ID No 430569.2.j.orf2 86 Ile Ser Val Val Ile Leu Thr Tyr Arg Ser Gln Val Pro Glu Asp 1 5 10 15 Phe Leu His His Ile Ser Val Glu Ile Leu Leu Arg Arg Ile Gln 20 25 30 Gln Ser Pro Leu Leu Leu Ser Lys Gly His Ser His Ile Phe Lys 35 40 45 87 91 PRT Homo sapiens misc_feature Incyte ID No 444689.1.j.orf2 87 Tyr Ala Gly Cys Cys Arg Asp Thr Arg Phe Pro Thr Pro Arg Xaa 1 5 10 15 Pro Gly Ser Leu Cys His Asn Phe Cys Arg Ser Ala Ala Cys Thr 20 25 30 Val Thr Arg Thr Ile His Gly Ser Pro Arg Glu Asp Thr Gly Thr 35 40 45 Pro Arg Ser Arg Glu Met Met Phe Gln Asp Ser Val Ala Phe Glu 50 55 60 Asp Val Ala Val Ser Phe Thr Gln Glu Glu Trp Ala Leu Leu Asp 65 70 75 Pro Ser Gln Lys Asn Leu Tyr Arg Asp Val Met Gln Glu Thr Phe 80 85 90 Lys 88 172 PRT Homo sapiens misc_feature Incyte ID No 445198.1.j.orf2 88 Leu Gln Lys Val Val Ile Leu Tyr Gly Ser Pro His Ser Phe Arg 1 5 10 15 Xaa Gln Gln Lys Met Asn Ile Ser Gln Ala Ser Val Ser Phe Lys 20 25 30 Asp Val Thr Ile Glu Phe Thr Gln Glu Glu Trp Gln Gln Met Ala 35 40 45 Pro Val Gln Lys Asn Leu Tyr Arg Asp Val Met Leu Glu Asn Tyr 50 55 60 Ser Asn Leu Val Ser Val Gly Tyr Cys Cys Phe Lys Pro Glu Val 65 70 75 Ile Phe Lys Leu Glu Gln Gly Glu Glu Pro Trp Phe Ser Glu Glu 80 85 90 Glu Phe Ser Asn Gln Ser His Pro Lys Asp Tyr Arg Gly Asp Asp 95 100 105 Leu Ile Lys Gln Asn Lys Lys Ile Lys Asp Lys His Leu Glu Gln 110 115 120 Ala Ile Cys Ile Asn Asn Lys Thr Leu Thr Thr Glu Glu Glu Lys 125 130 135 Val Leu Gly Lys Pro Phe Thr Leu His Val Ala Ala Val Ala Ser 140 145 150 Thr Lys Met Ser Cys Lys Cys Asn Ser Trp Glu Val Asn Leu Gln 155 160 165 Ser Ile Ser Glu Phe Ile Ile 170 89 66 PRT Homo sapiens misc_feature Incyte ID No 084399.1.orf1 89 Gly His Val Gln Ala Glu Ala Gly Glu Xaa Arg Ser Val Lys Val 1 5 10 15 Glu Glu Gly Glu Ala Ser Asp Phe Ser Leu Ala Trp Asp Ser Ser 20 25 30 Val Thr Ala Ala Gly Gly Leu Glu Gly Glu Pro Glu Cys Asp Gln 35 40 45 Xaa Thr Ser Arg Ala Leu Glu Xaa Arg Asn Ser Val Thr Ser Gln 50 55 60 Glu Glu Arg Asn Glu Gly 65 90 335 PRT Homo sapiens misc_feature Incyte ID No 350044.1.orf1 90 Leu Ala Glu Ala Leu Leu Met Asn Leu Thr Glu Gly Pro Leu Ala 1 5 10 15 Met Ala Glu Met Asp Pro Thr Gln Gly Arg Val Val Phe Glu Asp 20 25 30 Val Ala Ile Tyr Phe Ser Gln Glu Glu Trp Gly His Leu Asp Glu 35 40 45 Ala Gln Arg Leu Leu Tyr Arg Asp Val Met Leu Glu Asn Leu Ala 50 55 60 Leu Leu Ser Ser Leu Gly Ser Trp His Gly Ala Glu Asp Glu Glu 65 70 75 Ala Pro Ser Gln Gln Gly Phe Ser Val Gly Val Ser Glu Val Thr 80 85 90 Thr Ser Lys Pro Cys Leu Ser Ser Gln Lys Val His Pro Ser Glu 95 100 105 Thr Cys Gly Pro Pro Leu Lys Asp Ile Leu Cys Leu Val Glu His 110 115 120 Asn Gly Ile His Pro Glu Gln His Ile Tyr Ile Cys Glu Ala Glu 125 130 135 Leu Phe Gln His Pro Lys Gln Gln Ile Gly Glu Asn Leu Ser Arg 140 145 150 Gly Asp Asp Trp Ile Pro Ser Phe Gly Lys Asn His Arg Val His 155 160 165 Met Ala Glu Glu Ile Phe Thr Cys Met Glu Gly Trp Lys Asp Leu 170 175 180 Pro Ala Thr Ser Cys Leu Leu Gln His Gln Gly Pro Gln Ser Glu 185 190 195 Trp Lys Pro Tyr Arg Asp Thr Glu Asp Arg Glu Ala Phe Gln Thr 200 205 210 Gly Gln Asn Asp Tyr Lys Cys Ser Glu Cys Gly Lys Thr Phe Thr 215 220 225 Cys Ser Tyr Ser Phe Val Glu His Gln Lys Ile His Thr Gly Glu 230 235 240 Arg Ser Tyr Glu Cys Asn Lys Cys Gly Lys Phe Phe Lys Tyr Ser 245 250 255 Ala Asn Phe Xaa Lys His Gln Thr Val His Thr Ser Glu Arg Thr 260 265 270 Tyr Glu Cys Arg Glu Cys Gly Lys Ser Phe Met Tyr Asn Tyr Arg 275 280 285 Leu Met Arg His Lys Arg Val His Thr Gly Glu Arg Pro Tyr Glu 290 295 300 Cys Ser Glu Cys Gln Lys Ala Phe Ile Arg Lys Ser His Leu Val 305 310 315 His His Gln Lys Ile His Ser Glu Glu Arg Leu Val Cys Ser Met 320 325 330 Asn Val Gly Ile Leu 335 91 174 PRT Homo sapiens misc_feature Incyte ID No 441329.2.orf3 91 Arg Trp Lys Arg Lys Met Arg Lys Thr Thr Cys Gly Gly Arg Ile 1 5 10 15 Pro Pro Tyr Arg Thr Arg Leu Leu Gln Thr Gln Arg Tyr Ser Ala 20 25 30 Asn Ala Ser Gly Ala Ser Val Thr Arg Thr Leu Leu Gly Pro Arg 35 40 45 Glu Ala Leu Ser Arg Leu Lys Glu Leu Cys His Gln Trp Leu Arg 50 55 60 Pro Glu Ile Asn Thr Lys Glu Gln Ile Leu Glu Leu Leu Val Leu 65 70 75 Glu Gln Phe Leu Ser Ile Leu Pro Lys Glu Leu Gln Val Trp Leu 80 85 90 Gln Glu Tyr Arg Pro Asp Ser Gly Glu Glu Ala Val Thr Leu Leu 95 100 105 Glu Asp Leu Glu Leu Asp Leu Ser Gly Gln Gln Val Pro Gly Gln 110 115 120 Val His Gly Pro Glu Met Leu Ala Arg Gly Met Val Pro Leu Asp 125 130 135 Pro Val Gln Glu Ser Ser Ser Phe Asp Leu His His Glu Ala Thr 140 145 150 Gln Ser His Phe Lys His Ser Ser Arg Lys Pro Arg Leu Leu Gln 155 160 165 Ser Arg Gly Lys Lys Gln Gly Phe Ile 170 92 128 PRT Homo sapiens misc_feature Incyte ID No 442401.2.orf2 92 Met Cys Gln Gly Leu Leu Thr Phe Arg Asp Val Ala Ile Glu Phe 1 5 10 15 Ser Arg Glu Glu Trp Glu His Leu Asp Ser Asp Gln Lys Leu Leu 20 25 30 Tyr Gly Asp Val Met Leu Glu Asn Tyr Gly Asn Leu Val Ser Leu 35 40 45 Gly Leu Ala Val Ser Lys Pro Asp Leu Ile Thr Phe Leu Glu Gln 50 55 60 Arg Lys Glu Pro Trp Asn Val Lys Ser Ala Glu Thr Val Ala Ile 65 70 75 Gln Pro Asp Ile Phe Ser His Asp Thr Gln Gly Leu Leu Arg Lys 80 85 90 Lys Leu Ile Glu Ala Ser Phe Gln Lys Val Ile Leu Asp Gly Tyr 95 100 105 Gly Ser Cys Gly Pro Gln Asn Leu Asn Leu Arg Lys Glu Trp Glu 110 115 120 Ser Glu Gly Lys Ile Ile Leu Trp 125 93 110 PRT Homo sapiens misc_feature Incyte ID No 444933.2.orf1 93 Ser Cys Gly Arg Leu Ser Ser Ser Cys Glu Cys Lys Thr Met Ala 1 5 10 15 His Ala Leu Val Thr Phe Arg Asp Val Ala Ile Asp Phe Ser Gln 20 25 30 Lys Glu Trp Glu Cys Leu Asp Thr Thr Gln Arg Lys Leu Tyr Arg 35 40 45 Asp Val Met Leu Glu Asn Tyr Asn Asn Leu Val Ser Leu Gly Tyr 50 55 60 Ser Gly Ser Lys Pro Asp Val Ile Thr Leu Leu Glu Gln Gly Lys 65 70 75 Glu Pro Cys Val Val Ala Arg Asp Val Thr Gly Arg Gln Cys Pro 80 85 90 Gly Leu Leu Ser Arg His Lys Thr Lys Lys Leu Ser Ser Glu Lys 95 100 105 Asp Ile His Glu Ile 110 94 109 PRT Homo sapiens misc_feature Incyte ID No 481129.4.orf1 94 Arg Leu Ser Ala Gly Thr Ala Trp Pro Leu Gly Ser Gly Trp Pro 1 5 10 15 Thr Met Arg Thr Val Ala Ser Ala Gly Trp His Leu Thr Asp Ala 20 25 30 Ala Leu Thr Ala Arg Cys Pro Ala Thr Thr Ala Arg Trp Cys Gly 35 40 45 Ala Ser Ala Pro Thr Ala Ser Thr Cys Ile Ala Ser Ser Ser Gly 50 55 60 Cys Thr His Ser Arg Cys Ser Ser Thr Ala Pro Cys Ala Ala Arg 65 70 75 Asn Gly Ser Ser Arg Ser Glu Ala Arg Pro Gly Ser Arg Trp Arg 80 85 90 Gly Ile Leu Arg Leu Leu Pro His Ala Gly Ala Asp Gly Cys Trp 95 100 105 Gly Gln Arg Pro 95 236 PRT Homo sapiens misc_feature Incyte ID No 481999.1.orf2 95 Asp Ser Val Ala Leu Glu Asp Val Ala Val Asn Phe Thr Arg Glu 1 5 10 15 Glu Trp Ala Leu Leu Gly Pro Cys Gln Lys Asn Leu Tyr Lys Asp 20 25 30 Val Met Leu Glu Asn Tyr Met Asn Leu Ala Ser Val Glu Trp Glu 35 40 45 Ile Gln Pro Arg Thr Lys Arg Ser Ser Leu Gln Gln Gly Phe Leu 50 55 60 Lys Asn Gln Ile Phe Ser Gly Ile Gln Met Thr Arg Gly Tyr Ser 65 70 75 Gly Trp Lys Leu Cys Asp Cys Lys Asn Cys Gly Glu Val Phe Arg 80 85 90 Glu Gln Phe Cys Leu Lys Thr His Met Arg Val Gln Asn Gly Gly 95 100 105 Asn Thr Ser Glu Gly Asn Cys Tyr Gly Lys Asp Thr Leu Ser Val 110 115 120 His Lys Glu Ala Ser Thr Gly Gln Glu Leu Ser Lys Phe Asn Pro 125 130 135 Cys Gly Lys Val Phe Thr Leu Thr Pro Gly Leu Ala Val His Leu 140 145 150 Glu Val Leu Asn Ala Arg Gln Pro Tyr Lys Cys Lys Glu Cys Gly 155 160 165 Lys Gly Phe Lys Tyr Xaa Ala Ser Leu Asp Asn His Met Gly Ile 170 175 180 His Thr Asp Glu Lys Leu Xaa Glu Xaa Gln Xaa Tyr Gly Arg Ala 185 190 195 Val Thr Ala Ser Ser His Leu Xaa Gln Cys Val Ala Val Xaa Thr 200 205 210 Gly Xaa Xaa Ser Lys Lys Thr Lys Lys Cys Gly Lys Ser Phe Thr 215 220 225 Asn Xaa Ser Gln Leu Tyr Ala Pro Val Lys Thr 230 235 96 106 PRT Homo sapiens misc_feature Incyte ID No 233814.1.j.orf2 96 Met Ala Asp Lys Gln Ile Ser Leu Pro Ala Lys Leu Ile Asn Gly 1 5 10 15 Gly Ile Ala Gly Leu Ile Gly Val Thr Cys Val Phe Thr Ile Asp 20 25 30 Leu Ala Lys Thr Arg Leu Gln Asn Gln Gln Asn Gly Gln Arg Val 35 40 45 Tyr Thr Ser Met Ser Asp Cys Leu Ile Lys Thr Val Arg Ser Glu 50 55 60 Gly Tyr Phe Gly Met Tyr Arg Gly Ala Ala Val Asn Leu Thr Leu 65 70 75 Val Thr Pro Glu Lys Ala Ile Lys Leu Ala Ala Asn Asp Phe Phe 80 85 90 Arg His Gln Leu Ser Lys Asp Gly Gln Lys Leu Asp Pro Ala Leu 95 100 105 Lys 97 114 PRT Homo sapiens misc_feature Incyte ID No 351376.4.j.orf3 97 Gly Pro Cys Lys Pro Glu Ala Ser Ala Arg Ile Ser Pro Arg Met 1 5 10 15 Ser Thr Gly Ala Arg Ala Pro Ser Gly Lys Pro Val Gly Pro Ser 20 25 30 Glu Arg Glu Ser Arg Leu Lys Arg Asn Asp Ile Ser Asp Ile Thr 35 40 45 Gly Tyr Ala Leu Arg Ser Leu Trp Gly Glu Gly Leu Lys Leu Asn 50 55 60 Pro Glu Pro Pro Cys Pro Cys Arg Ala Gln Ser Arg Glu Gln Leu 65 70 75 Ala Ala Leu Lys Lys His His Glu Glu Glu Ile Val His His Lys 80 85 90 Lys Glu Ile Glu Arg Leu Gln Lys Glu Ile Glu Arg His Lys Gln 95 100 105 Lys Ile Lys Met Leu Lys His Asp Asp 110 98 293 PRT Homo sapiens misc_feature Incyte ID No 338992.1.orf1 98 Leu Met Pro Ser Arg Gly Leu Ile Met Thr Ser Pro Trp Arg Arg 1 5 10 15 Lys Leu Val Ile Leu Ile Leu Phe Ser Thr Thr Trp Cys Phe Glu 20 25 30 Trp His Phe Leu Glu Pro Leu Leu Val Trp Pro Met Trp Met Val 35 40 45 Leu Thr Phe Met Trp Ala Asn Thr Gly Asp Ser Arg Ala Met Leu 50 55 60 Gly Val Gln Glu Glu Asp Gly Ser Trp Ser Ala Val Thr Leu Ser 65 70 75 Asn Asp His Asn Ala Gln Asn Glu Arg Glu Leu Glu Arg Leu Lys 80 85 90 Leu Glu His Pro Lys Ser Glu Ala Lys Ser Val Val Lys Gln Asp 95 100 105 Arg Leu Leu Gly Leu Leu Met Pro Phe Arg Ala Phe Gly Asp Val 110 115 120 Lys Phe Lys Trp Ser Ile Asp Leu Gln Lys Arg Val Ile Glu Ser 125 130 135 Gly Pro Asp Gln Leu Asn Asp Asn Glu Tyr Thr Lys Phe Ile Pro 140 145 150 Pro Asn Tyr His Thr Pro Pro Tyr Leu Thr Ala Glu Pro Glu Val 155 160 165 Thr Tyr His Arg Leu Arg Pro Gln Asp Lys Phe Leu Val Leu Ala 170 175 180 Thr Asp Gly Leu Trp Glu Thr Met His Arg Gln Asp Val Val Arg 185 190 195 Ile Val Gly Glu Tyr Leu Thr Gly Met His His Gln Gln Pro Ile 200 205 210 Ala Val Gly Gly Tyr Lys Val Thr Leu Gly Gln Met His Gly Leu 215 220 225 Leu Thr Glu Arg Arg Thr Lys Met Ser Ser Val Phe Glu Asp Gln 230 235 240 Asn Ala Ala Thr His Leu Ile Arg His Ala Val Gly Asn Asn Glu 245 250 255 Phe Gly Thr Val Asp His Glu Arg Leu Ser Lys Met Leu Ser Leu 260 265 270 Pro Glu Glu Leu Ala Arg Met Tyr Arg Asp Asp Ile Thr Ile Ile 275 280 285 Val Val Gln Phe Asn Ser His Val 290 99 324 PRT Homo sapiens misc_feature Incyte ID No 200587.3.j.orf2 99 Pro Gly Ser Ser Gly Ala Gly Met Glu Ala Ala Val Ala Pro Gly 1 5 10 15 Arg Asp Ala Pro Ala Pro Ala Ala Ser Gln Pro Ser Gly Cys Gly 20 25 30 Lys His Asn Ser Pro Glu Arg Lys Val Tyr Met Asp Tyr Asn Ala 35 40 45 Thr Thr Pro Leu Glu Pro Glu Val Ile Gln Ala Met Thr Lys Ala 50 55 60 Met Trp Glu Ala Trp Gly Asn Pro Ser Ser Pro Tyr Ser Ala Gly 65 70 75 Arg Lys Ala Lys Asp Ile Ile Asn Ala Ala Arg Glu Ser Leu Ala 80 85 90 Lys Met Ile Gly Gly Lys Pro Gln Asp Ile Ile Phe Thr Ser Gly 95 100 105 Gly Thr Glu Ser Asn Asn Leu Val Ile His Ser Val Val Lys His 110 115 120 Phe His Ala Asn Gln Thr Ser Lys Gly His Thr Gly Gly His His 125 130 135 Ser Pro Val Lys Gly Ala Lys Pro His Phe Ile Thr Ser Ser Val 140 145 150 Glu His Asp Ser Ile Arg Leu Pro Leu Glu His Leu Val Glu Glu 155 160 165 Gln Val Ala Ala Val Thr Phe Val Pro Val Ser Lys Val Ser Gly 170 175 180 Gln Ala Glu Val Asp Asp Ile Leu Ala Ala Val Arg Pro Thr Thr 185 190 195 Arg Leu Val Thr Ile Met Leu Ala Asn Asn Glu Thr Gly Ile Val 200 205 210 Met Pro Val Pro Glu Ile Ser Gln Arg Ile Lys Ala Leu Asn Gln 215 220 225 Glu Arg Val Ala Ala Gly Leu Pro Pro Ile Leu Val His Thr Asp 230 235 240 Ala Ala Gln Ala Leu Gly Lys Gln Arg Val Asp Val Glu Asp Leu 245 250 255 Gly Val Asp Phe Leu Thr Ile Val Gly His Lys Phe Tyr Gly Pro 260 265 270 Arg Ile Gly Ala Leu Tyr Ile Arg Gly Leu Gly Glu Phe Thr Pro 275 280 285 Leu Tyr Pro Met Leu Phe Gly Gly Gly Gln Glu Arg Asn Phe Arg 290 295 300 Pro Gly Thr Glu Asn Thr Pro Met Ile Ala Gly Leu Gly Lys Val 305 310 315 Ser Pro Gly Glu Leu Glu Glu Met Ser 320 100 102 PRT Homo sapiens misc_feature Incyte ID No 246727.5.j.orf3 100 Asn Lys Met Lys Lys Val Arg Leu Lys Glu Leu Glu Ser Arg Leu 1 5 10 15 Gln Gln Val Asp Gly Phe Glu Lys Pro Lys Leu Leu Leu Glu Gln 20 25 30 Tyr Pro Thr Arg Pro His Ile Ala Ala Cys Met Leu Tyr Thr Ile 35 40 45 His Asn Thr Tyr Asp Asp Ile Glu Asn Lys Val Val Ala Asp Leu 50 55 60 Gly Cys Gly Cys Gly Val Leu Ser Ile Gly Thr Ala Met Leu Gly 65 70 75 Ala Gly Asp Arg Tyr Gly Phe Ser Lys Asp Cys Phe Gly Asn Gly 80 85 90 Lys Asn Ser Ser Ile Phe Leu Thr Gln Ile Leu Asn 95 100 101 391 PRT Homo sapiens misc_feature Incyte ID No 407087.3.j.orf2 101 Arg Glu Gln Val Arg Leu Glu Leu Ser Phe Val Asn Ser Asp Leu 1 5 10 15 Gln Met Leu Lys Glu Glu Leu Glu Gly Leu Asn Ile Ser Val Gly 20 25 30 Val Tyr Gln Asn Thr Glu Glu Ala Phe Thr Ile Pro Leu Ile Pro 35 40 45 Leu Gly Leu Lys Glu Thr Lys Asp Val Asp Phe Ala Val Val Leu 50 55 60 Lys Asp Phe Ile Leu Glu His Tyr Ser Glu Asp Gly Tyr Leu Tyr 65 70 75 Glu Asp Glu Ile Ala Asp Leu Met Asp Leu Arg Gln Ala Cys Arg 80 85 90 Thr Pro Ser Arg Asp Glu Ala Gly Val Glu Leu Leu Met Thr Tyr 95 100 105 Phe Ile Gln Leu Gly Phe Val Glu Ser Arg Phe Phe Pro Pro Thr 110 115 120 Arg Gln Met Gly Leu Leu Phe Thr Trp Tyr Asp Ser Leu Thr Gly 125 130 135 Val Pro Val Ser Gln Gln Asn Leu Leu Leu Glu Lys Ala Ser Val 140 145 150 Leu Phe Asn Thr Gly Ala Leu Tyr Thr Gln Ile Gly Thr Arg Cys 155 160 165 Asp Arg Gln Thr Gln Ala Gly Leu Glu Ser Ala Ile Asp Ala Phe 170 175 180 Gln Arg Ala Ala Gly Val Leu Asn Tyr Leu Lys Asp Thr Phe Thr 185 190 195 His Thr Pro Ser Tyr Asp Met Ser Pro Ala Met Leu Ser Val Leu 200 205 210 Val Lys Met Met Leu Ala Gln Ala Gln Glu Ser Val Phe Glu Lys 215 220 225 Ile Ser Leu Pro Gly Ile Arg Asn Glu Phe Phe Met Leu Val Lys 230 235 240 Val Ala Gln Glu Ala Ala Lys Val Gly Glu Val Tyr Gln Gln Leu 245 250 255 His Ala Ala Met Ser Gln Ala Pro Val Lys Asp Asn Ile Pro Tyr 260 265 270 Ser Trp Ala Ser Leu Ala Cys Val Lys Ala His His Tyr Ala Ala 275 280 285 Leu Ala His Tyr Phe Thr Ala Ile Leu Leu Xaa Asp His Gln Val 290 295 300 Lys Pro Gly Thr Asp Xaa Asp His Gln Glu Lys Cys Leu Ser Gln 305 310 315 Leu Tyr Asp His Met Pro Glu Gly Leu Thr Pro Leu Ala Thr Leu 320 325 330 Lys Asn Asp Gln Gln Arg Arg Gln Leu Gly Lys Ser His Leu Arg 335 340 345 Arg Ala Met Ala His Xaa Glu Glu Ser Val Arg Glu Ala Ser Leu 350 355 360 Cys Lys Lys Leu Arg Xaa Leu Arg Cys Tyr Arg Arg Cys Xaa Cys 365 370 375 Arg Thr Gly Thr Leu Pro Ala His Val Arg Pro Ala Pro Gly Gly 380 385 390 Gly 102 154 PRT Homo sapiens misc_feature Incyte ID No 441779.1.j.orf1 102 Ser Ser Glu Phe Gly Ser Arg Thr Gln Glu Ala Ile Met Val Leu 1 5 10 15 Ser Ala Ala Asp Lys Thr Asn Ile Lys Asn Cys Trp Gly Lys Ile 20 25 30 Gly Gly His Gly Gly Glu Tyr Gly Glu Glu Ala Leu Gln Arg Met 35 40 45 Phe Ala Ala Phe Pro Thr Thr Lys Thr Tyr Phe Ser His Ile Asp 50 55 60 Val Ser Pro Gly Ser Ala Gln Val Lys Ala His Gly Lys Lys Val 65 70 75 Ala Asp Ala Leu Ala Lys Ala Ala Asp His Val Glu Asp Leu Pro 80 85 90 Gly Ala Leu Ser Thr Leu Ser Asp Leu His Ala His Lys Leu Arg 95 100 105 Val Asp Pro Val Asn Phe Lys Phe Leu Ser His Cys Leu Leu Val 110 115 120 Thr Leu Ala Cys His His Pro Gly Asp Phe Thr Pro Ala Met His 125 130 135 Ala Ser Leu Asp Lys Phe Leu Ala Ser Val Ser Thr Val Leu Thr 140 145 150 Ser Lys Tyr Arg 103 199 PRT Homo sapiens misc_feature Incyte ID No 206603.1.orf2 103 Phe Pro Thr Arg Thr Leu Gly Ala Arg Ser Ser Pro Arg Pro Arg 1 5 10 15 Arg Ala Ala Asp Met Gly Asn Xaa Arg Glu His Trp Ile Arg Ser 20 25 30 Arg Pro Ile Ser Gly Arg Thr Thr Val Pro Leu Lys Leu Pro Met 35 40 45 Pro Glu Pro Gly Glu Leu Glu Glu Arg Phe Ala Ile Val Leu Asn 50 55 60 Ala Met Asn Leu Pro Pro Asp Lys Ala Arg Leu Leu Arg Gln Tyr 65 70 75 Asp Asn Glu Lys Lys Trp Glu Leu Ile Cys Asp Gln Glu Arg Phe 80 85 90 Gln Val Lys Asn Pro Pro His Thr Tyr Ile Gln Lys Leu Lys Gly 95 100 105 Tyr Leu Asp Pro Ala Val Thr Arg Lys Lys Phe Arg Arg Arg Val 110 115 120 Gln Glu Ser Thr Gln Val Leu Arg Glu Leu Glu Ile Ser Leu Arg 125 130 135 Thr Asn His Ile Gly Trp Val Arg Glu Phe Leu Asn Glu Glu Asn 140 145 150 Lys Gly Leu Asp Val Leu Val Glu Tyr Leu Ser Phe Ala Gln Tyr 155 160 165 Ala Arg Thr Phe Asp Phe Glu Ser Val Glu Ser Thr Val Glu Ser 170 175 180 Ser Val Asp Lys Ser Lys Pro Trp Ser Arg Ser Ile Glu Asp Leu 185 190 195 His Arg Gly Ser 104 476 PRT Homo sapiens misc_feature Incyte ID No 435694.2.orf3 104 Leu Leu Pro Tyr Ser Glu Val Val Leu Ala Leu Leu Thr Thr Leu 1 5 10 15 Phe Gln Gly Met Ile Thr Lys Thr His Lys Val Asp Leu Gly Leu 20 25 30 Pro Glu Lys Lys Lys Lys Lys Lys Val Val Lys Glu Pro Glu Thr 35 40 45 Arg Tyr Ser Val Leu Asn Asn Asp Asp Tyr Phe Ala Asp Val Ser 50 55 60 Pro Leu Arg Ala Thr Ser Pro Ser Lys Ser Val Ala His Gly Gln 65 70 75 Ala Pro Glu Met Pro Leu Val Lys Xaa Xaa Xaa Xaa Lys Lys Lys 80 85 90 Gly Val Ser Thr Leu Cys Glu Glu His Val Glu Pro Glu Thr Thr 95 100 105 Leu Pro Ala Arg Arg Thr Glu Lys Ser Pro Ser Leu Arg Lys Gln 110 115 120 Val Phe Gly His Leu Glu Phe Leu Ser Gly Glu Lys Lys Asn Lys 125 130 135 Lys Ser Pro Leu Ala Met Ser His Ala Ser Gly Val Lys Thr Ser 140 145 150 Pro Asp Pro Arg Gln Gly Glu Glu Glu Thr Arg Val Gly Lys Lys 155 160 165 Leu Lys Lys His Lys Lys Glu Lys Lys Gly Ala Gln Asp Pro Thr 170 175 180 Ala Phe Ser Val Gln Asp Pro Trp Phe Cys Glu Ala Arg Glu Ala 185 190 195 Arg Asp Val Gly Asp Thr Cys Ser Val Gly Lys Lys Asp Glu Glu 200 205 210 Gln Ala Ala Leu Gly Gln Lys Arg Lys Arg Lys Ser Pro Arg Glu 215 220 225 His Asn Gly Lys Val Lys Lys Lys Lys Lys Ile His Gln Glu Gly 230 235 240 Asp Ala Leu Pro Gly His Ser Lys Pro Ser Arg Ser Met Glu Ser 245 250 255 Ser Pro Arg Lys Gly Ser Lys Lys Lys Pro Val Lys Val Glu Ala 260 265 270 Pro Glu Tyr Ile Pro Ile Ser Asp Asp Pro Lys Ala Ser Ala Lys 275 280 285 Lys Lys Met Lys Ser Lys Lys Lys Val Glu Gln Pro Val Ile Glu 290 295 300 Glu Pro Ala Leu Lys Arg Lys Lys Lys Lys Lys Arg Lys Glu Ser 305 310 315 Gly Val Ala Gly Asp Pro Trp Lys Glu Glu Thr Asp Thr Asp Leu 320 325 330 Glu Val Val Leu Glu Lys Lys Gly Asn Met Asp Glu Ala His Ile 335 340 345 Asp Gln Val Arg Arg Lys Ala Leu Gln Glu Glu Ile Asp Arg Glu 350 355 360 Ser Gly Lys Thr Glu Ala Ser Glu Thr Arg Lys Trp Thr Gly Thr 365 370 375 Gln Phe Gly Gln Trp Asp Thr Ala Gly Phe Glu Asn Glu Asp Gln 380 385 390 Lys Leu Lys Phe Leu Arg Leu Met Gly Gly Phe Lys Asn Leu Ser 395 400 405 Pro Ser Phe Ser Arg Pro Ala Ser Thr Ile Ala Arg Pro Asn Met 410 415 420 Ala Leu Gly Lys Lys Ala Ala Asp Ser Leu Gln Gln Asn Leu Gln 425 430 435 Arg Asp Tyr Asp Arg Ala Met Ser Trp Lys Tyr Ser Arg Gly Ala 440 445 450 Gly Leu Gly Phe Ser Thr Ala Pro Asn Lys Ile Phe Tyr Ile Asp 455 460 465 Arg Asn Ala Ser Lys Ser Val Lys Leu Glu Asp 470 475 

What is claimed is:
 1. An isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of: a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-52, b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-52, c) a polynucleotide sequence complementary to a), d) a polynucleotide sequence complementary to b), and e) an RNA equivalent of a) through d).
 2. An isolated polynucleotide of claim 1, comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:1-52.
 3. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim
 1. 4. A composition for the detection of expression of diagnostic and therapeutic polynucleotides comprising at least one of the polynucleotides of claim 1 and a detectable label.
 5. A method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 1, the method comprising: a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
 6. A method for detecting a target polynucleotide in a sample, said target polynucleotide comprising a sequence of a polynucleotide of claim 1, the method comprising: a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
 7. A method of claim 5, wherein the probe comprises at least 30 contiguous nucleotides.
 8. A method of claim 5, wherein the probe comprises at least 60 contiguous nucleotides.
 9. A recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim
 1. 10. A cell transformed with a recombinant polynucleotide of claim
 9. 11. A transgenic organism comprising a recombinant polynucleotide of claim
 9. 12. A method for producing a diagnostic and therapeutic polypeptide, the method comprising: a) culturing a cell under conditions suitable for expression of the diagnostic and therapeutic polypeptide, wherein said cell is transformed with a recombinant polynucleotide of claim 9, and b) recovering the diagnostic and therapeutic polypeptide so expressed.
 13. A purified diagnostic and therapeutic polypeptide (DITHP) encoded by at least one of the polynucleotides of claim
 2. 14. An isolated antibody which specifically binds to a diagnostic and therapeutic polypeptide of claim
 13. 15. A method of identifying a test compound which specifically binds to the diagnostic and therapeutic polypeptide of claim 13, the method comprising the steps of: a) providing a test compound; b) combining the diagnostic and therapeutic polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the diagnostic and therapeutic polypeptide to the test compound, thereby identifying the test compound which specifically binds the diagnostic and therapeutic polypeptide.
 16. A microarray wherein at least one element of the microarray is a polynucleotide of claim
 3. 17. A method for generating a transcript image of a sample which contains polynucleotides, the method comprising the steps of: a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray of claim 16 with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
 18. A method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence of claim 1, the method comprising: a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
 19. A method of claim 6 for toxicity testing of a compound, further comprising: c) comparing the presence, absence or amount of said target polynucleotide in a first biological sample and a second biological sample, wherein said first biological sample has been contacted with said compound, and said second sample is a control, whereby a change in presence, absence or amount of said target polynucleotide in said first sample, as compared with said second sample, is indicative of toxic response to said compound. 